diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index d7eb60c..0000000 --- a/.travis.yml +++ /dev/null @@ -1,21 +0,0 @@ -language: perl -os: linux -dist: bionic -services: docker - -branches: - only: - - main - -install: - - docker build -t vcf2maf:main . - - docker image prune -f - - wget -P tests https://data.cyri.ac/Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz - - gzip -d tests/Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz - - wget -P tests https://data.cyri.ac/homo_sapiens_vep_102_GRCh38_chr21.tar.gz - - tar -zxf tests/homo_sapiens_vep_102_GRCh38_chr21.tar.gz -C tests - -script: - - perl tests/vcf2maf.t - - perl tests/vcf2vcf.t - - perl tests/maf2vcf.t diff --git a/Dockerfile b/Dockerfile index 1d2daa3..f2a7e24 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,7 @@ FROM clearlinux:latest AS builder # Install a minimal versioned OS into /install_root, and bundled tools if any -ENV CLEAR_VERSION=33980 +ENV CLEAR_VERSION=41780 RUN swupd os-install --no-progress --no-boot-update --no-scripts \ --version ${CLEAR_VERSION} \ --path /install_root \ @@ -9,18 +9,20 @@ RUN swupd os-install --no-progress --no-boot-update --no-scripts \ --bundles os-core-update,which # Download and install conda into /usr/bin -ENV MINICONDA_VERSION=py37_4.9.2 -RUN swupd bundle-add --no-progress curl && \ - curl -sL https://repo.anaconda.com/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -o /tmp/miniconda.sh && \ - sh /tmp/miniconda.sh -bfp /usr +ENV MINICONDA_VERSION=py312_24.4.0-0 +RUN curl -sL https://repo.anaconda.com/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -o /tmp/miniconda.sh && \ + bash /tmp/miniconda.sh -bup /usr && \ + rm -f /tmp/miniconda.sh && \ + conda config --set solver libmamba -# Use conda to install remaining tools/dependencies into /usr/local -ENV VEP_VERSION=102.0 \ - HTSLIB_VERSION=1.10.2 \ - BCFTOOLS_VERSION=1.10.2 \ - SAMTOOLS_VERSION=1.10 \ - LIFTOVER_VERSION=377 -RUN conda create -qy -p /usr/local \ +# Use mamba to install remaining tools/dependencies into /usr/local +ENV VEP_VERSION=112.0 \ + HTSLIB_VERSION=1.20 \ + BCFTOOLS_VERSION=1.20 \ + SAMTOOLS_VERSION=1.20 \ + LIFTOVER_VERSION=447 +RUN conda create -y -p /usr/local && \ + conda install -y -p /usr/local \ -c conda-forge \ -c bioconda \ -c defaults \ diff --git a/LICENSE b/LICENSE index 6dfe65e..b7c2c3b 100644 --- a/LICENSE +++ b/LICENSE @@ -1,4 +1,4 @@ -Copyright 2021 Memorial Sloan Kettering Cancer Center +Copyright 2024 Memorial Sloan Kettering Cancer Center Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/README.md b/README.md index c89917d..f0e2ec5 100644 --- a/README.md +++ b/README.md @@ -1,21 +1,19 @@ vcfmaf ======= -To convert a [VCF](http://samtools.github.io/hts-specs/) into a [MAF](https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format), each variant must be mapped to only one of all possible gene transcripts/isoforms that it might affect. But even within a single isoform, a `Missense_Mutation` close enough to a `Splice_Site`, can be labeled as either in MAF format, but not as both. **This selection of a single effect per variant, is often subjective. And that's what this project attempts to standardize.** The `vcf2maf` and `maf2maf` scripts leave most of that responsibility to [Ensembl's VEP](http://useast.ensembl.org/info/docs/tools/vep/index.html), but allows you to override their "canonical" isoforms, or use a custom ExAC VCF for annotation. Though the most useful feature is the **extensive support in parsing a wide range of crappy MAF-like or VCF-like formats** we've seen out in the wild. - -[![Build Status](https://travis-ci.com/mskcc/vcf2maf.svg?branch=master)](https://travis-ci.com/mskcc/vcf2maf) +To convert a [VCF](https://samtools.github.io/hts-specs//) into a [MAF](https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format), each variant must be mapped to only one of all possible gene transcripts/isoforms that it might affect. But even within a single isoform, a `Missense_Mutation` close enough to a `Splice_Site`, can be labeled as either in MAF format, but not as both. **This selection of a single effect per variant, is often subjective. And that's what this project attempts to standardize.** The `vcf2maf` and `maf2maf` scripts leave most of that responsibility to [Ensembl's VEP](http://ensembl.org/info/docs/tools/vep/index.html), but allows you to override their "canonical" isoforms, or use a custom ExAC VCF for annotation. Though the most useful feature is the **extensive support in parsing a wide range of crappy MAF-like or VCF-like formats** we've seen out in the wild. Quick start ----------- -Find the [latest stable release](https://github.com/mskcc/vcf2maf/releases), download it, and view the detailed usage manuals for `vcf2maf` and `maf2maf`: +Find the [latest release](https://github.com/mskcc/vcf2maf/releases), download it, and view the detailed usage manuals for `vcf2maf` and `maf2maf`: export VCF2MAF_URL=`curl -sL https://api.github.com/repos/mskcc/vcf2maf/releases | grep -m1 tarball_url | cut -d\" -f4` curl -L -o mskcc-vcf2maf.tar.gz $VCF2MAF_URL; tar -zxf mskcc-vcf2maf.tar.gz; cd mskcc-vcf2maf-* perl vcf2maf.pl --man perl maf2maf.pl --man -If you don't have [VEP](http://useast.ensembl.org/info/docs/tools/vep/index.html) installed, then [follow this gist](https://gist.github.com/ckandoth/61c65ba96b011f286220fa4832ad2bc0). Of the many annotators out there, VEP is preferred for its large team of active coders, and its CLIA-compliant [HGVS formats](http://www.hgvs.org/mutnomen/recs.html). After installing VEP, test out `vcf2maf` like this: +If you don't have VEP installed, then [follow this gist](https://gist.github.com/ckandoth/4bccadcacd58aad055ed369a78bf2e7c). Of the many annotators out there, VEP is preferred for its large team of active coders, and its CLIA-compliant [HGVS formats](http://www.hgvs.org/mutnomen/recs.html). After installing VEP, test out `vcf2maf` like this: perl vcf2maf.pl --input-vcf tests/test.vcf --output-maf tests/test.vep.maf @@ -49,6 +47,37 @@ After tests on variant lists from many sources, `maf2vcf` and `maf2maf` are quit See `data/minimalist_test_maf.tsv` for a sampler. Addition of `Tumor_Seq_Allele1` will be used to determine zygosity. Otherwise, it will try to determine zygosity from variant allele fractions, assuming that arguments `--tum-vad-col` and `--tum-depth-col` are set correctly to the names of columns containing those read counts. Specifying the `Matched_Norm_Sample_Barcode` with its respective columns containing read-counts, is also strongly recommended. Columns containing normal allele read counts can be specified using argument `--nrm-vad-col` and `--nrm-depth-col`. +Docker +------ + +Assuming you have a recent version of docker, clone the main branch and build an image as follows: + + git clone git@github.com:mskcc/vcf2maf.git + cd vcf2maf + docker build -t vcf2maf:main . + docker builder prune -f + +Now you run the scripts in docker as follows: + + docker run --rm vcf2maf:main perl vcf2maf.pl --help + docker run --rm vcf2maf:main perl maf2maf.pl --help + +Testing +------- + +A small standalone test dataset was created by restricting VEP v112 cache/fasta to chr21 in GRCh38 and hosting that on a private server for download by CI services. We can manually fetch those as follows: + + wget -P tests https://data.cyri.ac/Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz + gzip -d tests/Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz + wget -P tests https://data.cyri.ac/homo_sapiens_vep_112_GRCh38_chr21.tar.gz + tar -zxf tests/homo_sapiens_vep_112_GRCh38_chr21.tar.gz -C tests + +And the following scripts test the docker image on predefined inputs and compare outputs against expected outputs: + + perl tests/vcf2maf.t + perl tests/vcf2vcf.t + perl tests/maf2vcf.t + License ------- @@ -57,4 +86,4 @@ License Citation -------- - Cyriac Kandoth. mskcc/vcf2maf: vcf2maf v1.6.19. (2020). doi:10.5281/zenodo.593251 + Cyriac Kandoth. mskcc/vcf2maf: vcf2maf v1.6. (2020). doi:10.5281/zenodo.593251 diff --git a/maf2maf.pl b/maf2maf.pl index ead44c8..74681c4 100755 --- a/maf2maf.pl +++ b/maf2maf.pl @@ -16,7 +16,7 @@ my ( $tum_depth_col, $tum_rad_col, $tum_vad_col ) = qw( t_depth t_ref_count t_alt_count ); my ( $nrm_depth_col, $nrm_rad_col, $nrm_vad_col ) = qw( n_depth n_ref_count n_alt_count ); my ( $vep_path, $vep_data, $vep_forks, $buffer_size, $any_allele ) = ( "$ENV{HOME}/miniconda3/bin", "$ENV{HOME}/.vep", 4, 5000, 0 ); -my ( $ref_fasta, $filter_vcf ) = ( "$ENV{HOME}/.vep/homo_sapiens/102_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz", "" ); +my ( $ref_fasta, $filter_vcf ) = ( "$ENV{HOME}/.vep/homo_sapiens/112_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz", "" ); my ( $species, $ncbi_build, $cache_version, $maf_center, $max_subpop_af ) = ( "homo_sapiens", "GRCh37", "", ".", 0.0004 ); my $perl_bin = $Config{perlpath}; @@ -41,8 +41,9 @@ MINIMISED ExAC_AF ExAC_AF_AFR ExAC_AF_AMR ExAC_AF_EAS ExAC_AF_FIN ExAC_AF_NFE ExAC_AF_OTH ExAC_AF_SAS GENE_PHENO FILTER flanking_bps variant_id variant_qual ExAC_AF_Adj ExAC_AC_AN_Adj ExAC_AC_AN ExAC_AC_AN_AFR ExAC_AC_AN_AMR ExAC_AC_AN_EAS ExAC_AC_AN_FIN ExAC_AC_AN_NFE - ExAC_AC_AN_OTH ExAC_AC_AN_SAS ExAC_FILTER gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF - gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF ); + ExAC_AC_AN_OTH ExAC_AC_AN_SAS ExAC_FILTER gnomADe_AF gnomADe_AFR_AF gnomADe_AMR_AF + gnomADe_ASJ_AF gnomADe_EAS_AF gnomADe_FIN_AF gnomADe_NFE_AF gnomADe_OTH_AF gnomADe_SAS_AF +); # Check for missing or crappy arguments unless( @ARGV and $ARGV[0]=~m/^-/ ) { @@ -382,7 +383,7 @@ =head1 OPTIONS --species Ensembl-friendly name of species (e.g. mus_musculus for mouse) [homo_sapiens] --ncbi-build NCBI reference assembly of variants in MAF (e.g. GRCm38 for mouse) [GRCh37] --cache-version Version of offline cache to use with VEP (e.g. 75, 84, 91) [Default: Installed version] - --ref-fasta Reference FASTA file [~/.vep/homo_sapiens/102_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz] + --ref-fasta Reference FASTA file [~/.vep/homo_sapiens/112_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz] --help Print a brief help message and quit --man Print the detailed manual @@ -401,7 +402,6 @@ =head2 Relevant links: =head1 AUTHORS Cyriac Kandoth (ckandoth@gmail.com) - Qingguo Wang (josephw10000@gmail.com) =head1 LICENSE diff --git a/maf2vcf.pl b/maf2vcf.pl index c071da1..5ae9ce8 100644 --- a/maf2vcf.pl +++ b/maf2vcf.pl @@ -9,7 +9,7 @@ use Pod::Usage qw( pod2usage ); # Set any default paths and constants -my $ref_fasta = "$ENV{HOME}/.vep/homo_sapiens/102_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz"; +my $ref_fasta = "$ENV{HOME}/.vep/homo_sapiens/112_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz"; my ( $tum_depth_col, $tum_rad_col, $tum_vad_col ) = qw( t_depth t_ref_count t_alt_count ); my ( $nrm_depth_col, $nrm_rad_col, $nrm_vad_col ) = qw( n_depth n_ref_count n_alt_count ); @@ -357,7 +357,7 @@ =head1 OPTIONS --input-maf Path to input file in MAF format --output-dir Path to output directory where VCFs will be stored, one per TN-pair --output-vcf Path to output multi-sample VCF containing all TN-pairs [/.vcf] - --ref-fasta Path to reference Fasta file [~/.vep/homo_sapiens/102_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz] + --ref-fasta Path to reference Fasta file [~/.vep/homo_sapiens/112_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz] --per-tn-vcfs Specify this to generate VCFs per-TN pair, in addition to the multi-sample VCF --tum-depth-col Name of MAF column for read depth in tumor BAM [t_depth] --tum-rad-col Name of MAF column for reference allele depth in tumor BAM [t_ref_count] @@ -376,12 +376,11 @@ =head2 Relevant links: Homepage: https://github.com/ckandoth/vcf2maf VCF format: http://samtools.github.io/hts-specs/ - MAF format: https://wiki.nci.nih.gov/x/eJaPAQ + MAF format: https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format =head1 AUTHORS Cyriac Kandoth (ckandoth@gmail.com) - Qingguo Wang (josephw10000@gmail.com) =head1 LICENSE diff --git a/tests/test_b38_output.maf b/tests/test_b38_output.maf index 16de65c..5823520 100644 --- a/tests/test_b38_output.maf +++ b/tests/test_b38_output.maf @@ -1,27 +1,27 @@ #version 2.4 -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND_VEP SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS AF AFR_AF AMR_AF ASN_AF EAS_AF EUR_AF SAS_AF AA_AF EA_AF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO MINIMISED GENE_PHENO FILTER flanking_bps vcf_id vcf_qual gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF vcf_pos -RUNX1 861 . GRCh38 21 34792292 34792292 + Missense_Mutation SNP A A C novel TUMOR NORMAL A A c.1286T>G p.Leu429Arg p.L429R ENST00000300305 8/8 54 . 21 0 . . RUNX1,missense_variant,p.Leu402Arg,ENST00000344691,NM_001001890.3;RUNX1,missense_variant,p.Leu429Arg,ENST00000300305,;RUNX1,missense_variant,p.Leu429Arg,ENST00000675419,NM_001754.5;RUNX1,missense_variant,p.Leu429Arg,ENST00000437180,;RUNX1,missense_variant,p.Leu338Arg,ENST00000399240,;RUNX1,3_prime_UTR_variant,,ENST00000482318,; C ENSG00000159216 ENST00000300305 Transcript missense_variant 1731/6222 1286/1443 429/480 L/R cTg/cGg 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196.238 UPI000015FE6A deleterious(0) possibly_damaging(0.887) 8/8 PANTHER:PTHR11950:SF40,PANTHER:PTHR11950,PIRSF:PIRSF009374,Pfam:PF08504,Prints:PR00967 MODERATE 1 SNV 1 1 . CAG . . 34792292 -RUNX1 861 . GRCh38 21 34792478 34792478 + Missense_Mutation SNP C C T rs867474432 TUMOR NORMAL C C c.1100G>A p.Gly367Asp p.G367D ENST00000300305 8/8 901 778 123 482 482 0 RUNX1,missense_variant,p.Gly340Asp,ENST00000344691,NM_001001890.3;RUNX1,missense_variant,p.Gly367Asp,ENST00000300305,;RUNX1,missense_variant,p.Gly367Asp,ENST00000675419,NM_001754.5;RUNX1,missense_variant,p.Gly367Asp,ENST00000437180,;RUNX1,missense_variant,p.Gly276Asp,ENST00000399240,;RUNX1,3_prime_UTR_variant,,ENST00000482318,; T ENSG00000159216 ENST00000300305 Transcript missense_variant 1545/6222 1100/1443 367/480 G/D gGc/gAc rs867474432,COSV55867253 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196.238 UPI000015FE6A deleterious(0.01) possibly_damaging(0.568) 8/8 Low_complexity_(Seg):seg,PANTHER:PTHR11950:SF40,PANTHER:PTHR11950,PIRSF:PIRSF009374,Gene3D:4.10.770.10 0,1 MODERATE 1 SNV 1 0,1 1 . GCC . . 34792478 -RUNX1 861 . GRCh38 21 34880549 34880549 + Splice_Region SNP T T C novel TUMOR NORMAL T T c.508+8A>G ENST00000300305 504 450 54 0 . . RUNX1,splice_region_variant,,ENST00000300305,;RUNX1,splice_region_variant,,ENST00000344691,NM_001001890.3;RUNX1,splice_region_variant,,ENST00000358356,NM_001122607.2;RUNX1,splice_region_variant,,ENST00000399237,;RUNX1,splice_region_variant,,ENST00000399240,;RUNX1,splice_region_variant,,ENST00000437180,;RUNX1,splice_region_variant,,ENST00000675419,NM_001754.5;RUNX1,downstream_gene_variant,,ENST00000455571,;AP000331.1,intron_variant,,ENST00000651798,;RUNX1,splice_region_variant,,ENST00000482318,; C ENSG00000159216 ENST00000300305 Transcript splice_region_variant,intron_variant 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196.238 UPI000015FE6A 4/7 LOW 1 SNV 1 1 . ATA . . 34880549 -RUNX1 861 . GRCh38 21 34880555 34880556 + Splice_Site INS - - CCTCTT novel TUMOR NORMAL - - c.504_508+1dup p.X168_splice ENST00000300305 883 658 225 343 343 0 RUNX1,splice_donor_variant,,ENST00000300305,;RUNX1,splice_donor_variant,,ENST00000344691,NM_001001890.3;RUNX1,splice_donor_variant,,ENST00000358356,NM_001122607.2;RUNX1,splice_donor_variant,,ENST00000399237,;RUNX1,splice_donor_variant,,ENST00000399240,;RUNX1,splice_donor_variant,,ENST00000437180,;RUNX1,splice_donor_variant,,ENST00000675419,NM_001754.5;RUNX1,downstream_gene_variant,,ENST00000455571,;AP000331.1,intron_variant,,ENST00000651798,;RUNX1,splice_donor_variant,,ENST00000482318,; CCTCTT ENSG00000159216 ENST00000300305 Transcript splice_donor_variant 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196.238 UPI000015FE6A 4/7 HIGH 1 insertion 1 1 . TAC . . 34880555 -RUNX1 861 . GRCh38 21 34880595 34880595 + Missense_Mutation SNP C C T TUMOR NORMAL C C c.470G>A p.Arg157Lys p.R157K ENST00000300305 4/8 862 788 74 523 522 1 RUNX1,missense_variant,p.Arg130Lys,ENST00000344691,NM_001001890.3;RUNX1,missense_variant,p.Arg157Lys,ENST00000300305,;RUNX1,missense_variant,p.Arg157Lys,ENST00000675419,NM_001754.5;RUNX1,missense_variant,p.Arg157Lys,ENST00000437180,;RUNX1,missense_variant,p.Arg130Lys,ENST00000358356,NM_001122607.2;RUNX1,missense_variant,p.Arg130Lys,ENST00000399240,;RUNX1,missense_variant,p.Arg145Lys,ENST00000399237,;RUNX1,downstream_gene_variant,,ENST00000455571,;AP000331.1,intron_variant,,ENST00000651798,;RUNX1,3_prime_UTR_variant,,ENST00000482318,; T ENSG00000159216 ENST00000300305 Transcript missense_variant 915/6222 470/1443 157/480 R/K aGa/aAa COSV55871984,COSV55885034 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196.238 UPI000015FE6A tolerated(0.16) probably_damaging(0.978) 4/8 PROSITE_profiles:PS51062,PANTHER:PTHR11950:SF40,PANTHER:PTHR11950,PIRSF:PIRSF009374,Gene3D:2.60.40.720,Pfam:PF00853,Superfamily:SSF49417,Prints:PR00967 1,1 MODERATE 1 SNV 1 1,1 1 . TCT . . 34880595 -RUNX1 861 . GRCh38 21 34880650 34880651 + Frame_Shift_Ins INS - - G novel TUMOR NORMAL - - c.414_415insC p.Asn139GlnfsTer5 p.N139Qfs*5 ENST00000300305 4/8 611 449 162 528 527 1 RUNX1,frameshift_variant,p.Asn112GlnfsTer5,ENST00000344691,NM_001001890.3;RUNX1,frameshift_variant,p.Asn139GlnfsTer5,ENST00000300305,;RUNX1,frameshift_variant,p.Asn139GlnfsTer5,ENST00000675419,NM_001754.5;RUNX1,frameshift_variant,p.Asn139GlnfsTer5,ENST00000437180,;RUNX1,frameshift_variant,p.Asn112GlnfsTer5,ENST00000358356,NM_001122607.2;RUNX1,frameshift_variant,p.Asn112GlnfsTer5,ENST00000399240,;RUNX1,frameshift_variant,p.Asn127GlnfsTer5,ENST00000399237,;RUNX1,frameshift_variant,p.Asn126GlnfsTer5,ENST00000455571,;AP000331.1,intron_variant,,ENST00000651798,;RUNX1,3_prime_UTR_variant,,ENST00000482318,; G ENSG00000159216 ENST00000300305 Transcript frameshift_variant 859-860/6222 414-415/1443 138-139/480 -/X -/C 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196.238 UPI000015FE6A 4/8 PROSITE_profiles:PS51062,PANTHER:PTHR11950:SF40,PANTHER:PTHR11950,PIRSF:PIRSF009374,Gene3D:2.60.40.720,Pfam:PF00853,Superfamily:SSF49417,Prints:PR00967 HIGH 1 insertion 1 1 . TTT . . 34880650 -RUNX1 861 . GRCh38 21 34886911 34886911 + Missense_Mutation SNP G G A novel TUMOR NORMAL G G c.283C>T p.Pro95Ser p.P95S ENST00000300305 3/8 51 34 17 0 . . RUNX1,missense_variant,p.Pro68Ser,ENST00000344691,NM_001001890.3;RUNX1,missense_variant,p.Pro95Ser,ENST00000300305,;RUNX1,missense_variant,p.Pro95Ser,ENST00000675419,NM_001754.5;RUNX1,missense_variant,p.Pro95Ser,ENST00000437180,;RUNX1,missense_variant,p.Pro68Ser,ENST00000358356,NM_001122607.2;RUNX1,missense_variant,p.Pro68Ser,ENST00000399240,;RUNX1,missense_variant,p.Pro83Ser,ENST00000399237,;RUNX1,missense_variant,p.Pro82Ser,ENST00000455571,;RUNX1,downstream_gene_variant,,ENST00000475045,;AP000331.1,downstream_gene_variant,,ENST00000651798,;RUNX1,intron_variant,,ENST00000482318,;,regulatory_region_variant,,ENSR00000141768,; A ENSG00000159216 ENST00000300305 Transcript missense_variant 728/6222 283/1443 95/480 P/S Ccc/Tcc 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196.238 UPI000015FE6A deleterious(0) probably_damaging(0.997) 3/8 PROSITE_profiles:PS51062,PANTHER:PTHR11950:SF40,PANTHER:PTHR11950,PIRSF:PIRSF009374,Gene3D:2.60.40.720,Pfam:PF00853,Superfamily:SSF49417,Prints:PR00967,Prints:PR00967 MODERATE 1 SNV 1 1 . GGG . . 34886911 -SETD4 54093 . GRCh38 21 36043782 36043782 + Missense_Mutation SNP C C G novel TUMOR NORMAL C C c.901G>C p.Glu301Gln p.E301Q ENST00000399215 6/10 1140 1010 130 975 975 0 SETD4,missense_variant,p.Glu301Gln,ENST00000399215,;SETD4,missense_variant,p.Glu277Gln,ENST00000399212,NM_001286752.2;SETD4,missense_variant,p.Glu301Gln,ENST00000332131,NM_017438.5;SETD4,missense_variant,p.Gly277Arg,ENST00000399201,;SETD4,missense_variant,p.Gly277Arg,ENST00000399205,NM_001007261.2;SETD4,missense_variant,p.Gly301Arg,ENST00000399208,NM_001007259.2;SETD4,missense_variant,p.Gly301Arg,ENST00000399207,;SETD4,downstream_gene_variant,,ENST00000424303,;SETD4,downstream_gene_variant,,ENST00000429161,;SETD4,downstream_gene_variant,,ENST00000442559,;SETD4,downstream_gene_variant,,ENST00000446166,;SETD4,splice_region_variant,,ENST00000481477,;SETD4,upstream_gene_variant,,ENST00000469482,;SETD4,downstream_gene_variant,,ENST00000485865,;SETD4,upstream_gene_variant,,ENST00000487297,; G ENSG00000185917 ENST00000399215 Transcript missense_variant,splice_region_variant 2274/4272 901/1323 301/440 E/Q Gaa/Caa 1 -1 SETD4 HGNC HGNC:1258 protein_coding YES CCDS13640.1 ENSP00000382163 Q9NVD3.158 UPI000012868E deleterious(0.01) benign(0.203) 6/10 PANTHER:PTHR13271,PANTHER:PTHR13271:SF8,PIRSF:PIRSF027158 MODERATE 1 SNV 2 . CCT . . 36043782 -ERG 2078 . GRCh38 21 38383625 38383625 + Silent SNP T T C novel TUMOR NORMAL T T c.1239A>G p.Ser413= p.S413= ENST00000417133 12/12 352 329 23 0 . . ERG,synonymous_variant,p.Ser389=,ENST00000442448,NM_004449.4;ERG,synonymous_variant,p.Ser413=,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,synonymous_variant,p.Ser390=,ENST00000398910,NM_001291391.1;ERG,synonymous_variant,p.Ser389=,ENST00000398911,;ERG,synonymous_variant,p.Ser406=,ENST00000288319,NM_182918.4;ERG,synonymous_variant,p.Ser383=,ENST00000398907,;ERG,synonymous_variant,p.Ser382=,ENST00000398905,NM_001331025.2;ERG,synonymous_variant,p.Ser290=,ENST00000398897,NM_001243429.1;ERG,synonymous_variant,p.Ser413=,ENST00000398919,NM_001243428.1;ERG,synonymous_variant,p.Ser314=,ENST00000453032,NM_001136155.1; C ENSG00000157554 ENST00000417133 Transcript synonymous_variant 1425/5023 1239/1461 413/486 S tcA/tcG 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS46648.1 ENSP00000414150 P11308.209 UPI000018681C NM_001243432.2,NM_001136154.1 12/12 PANTHER:PTHR11849,PANTHER:PTHR11849:SF216,Superfamily:SSF46785 LOW 1 SNV 2 1 . ATG . . 38383625 -ERG 2078 . GRCh38 21 38400597 38400597 + Missense_Mutation SNP G G A TUMOR NORMAL G G c.743C>T p.Thr248Met p.T248M ENST00000417133 8/12 1199 892 307 567 566 1 ERG,missense_variant,p.Thr248Met,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,missense_variant,p.Thr248Met,ENST00000398910,NM_001291391.1;ERG,missense_variant,p.Thr241Met,ENST00000288319,NM_182918.4;ERG,missense_variant,p.Thr241Met,ENST00000398907,;ERG,missense_variant,p.Thr248Met,ENST00000398919,NM_001243428.1;ERG,missense_variant,p.Thr149Met,ENST00000453032,NM_001136155.1;ERG,missense_variant,p.Thr209Met,ENST00000429727,;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398905,NM_001331025.2;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,non_coding_transcript_exon_variant,,ENST00000492833,;ERG,intron_variant,,ENST00000481609,;ERG,downstream_gene_variant,,ENST00000473107,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,;,regulatory_region_variant,,ENSR00000662899,; A ENSG00000157554 ENST00000417133 Transcript missense_variant 929/5023 743/1461 248/486 T/M aCg/aTg COSV55741264 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS46648.1 ENSP00000414150 P11308.209 UPI000018681C NM_001243432.2,NM_001136154.1 tolerated(0.19) benign(0.39) 8/12 PANTHER:PTHR11849,PANTHER:PTHR11849:SF216 1 MODERATE 1 SNV 2 1 1 . CGT . . 38400597 -ERG 2078 . GRCh38 21 38400606 38400606 + Missense_Mutation SNP G G T TUMOR NORMAL G G c.734C>A p.Pro245His p.P245H ENST00000417133 8/12 343 190 153 507 507 0 ERG,missense_variant,p.Pro245His,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,missense_variant,p.Pro245His,ENST00000398910,NM_001291391.1;ERG,missense_variant,p.Pro238His,ENST00000288319,NM_182918.4;ERG,missense_variant,p.Pro238His,ENST00000398907,;ERG,missense_variant,p.Pro245His,ENST00000398919,NM_001243428.1;ERG,missense_variant,p.Pro146His,ENST00000453032,NM_001136155.1;ERG,missense_variant,p.Pro206His,ENST00000429727,;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398905,NM_001331025.2;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,non_coding_transcript_exon_variant,,ENST00000492833,;ERG,intron_variant,,ENST00000481609,;ERG,downstream_gene_variant,,ENST00000473107,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,;,regulatory_region_variant,,ENSR00000662899,; T ENSG00000157554 ENST00000417133 Transcript missense_variant 920/5023 734/1461 245/486 P/H cCt/cAt COSV55741651 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS46648.1 ENSP00000414150 P11308.209 UPI000018681C NM_001243432.2,NM_001136154.1 tolerated(0.1) benign(0.227) 8/12 PANTHER:PTHR11849,PANTHER:PTHR11849:SF216 1 MODERATE 1 SNV 2 1 1 . AGG . . 38400606 -ERG 2078 . GRCh38 21 38403659 38403659 + Missense_Mutation SNP C C T novel TUMOR NORMAL C C c.460G>A p.Val154Met p.V154M ENST00000417133 6/12 287 149 138 0 . . ERG,missense_variant,p.Val154Met,ENST00000442448,NM_004449.4;ERG,missense_variant,p.Val154Met,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,missense_variant,p.Val154Met,ENST00000398910,NM_001291391.1;ERG,missense_variant,p.Val154Met,ENST00000398911,;ERG,missense_variant,p.Val147Met,ENST00000288319,NM_182918.4;ERG,missense_variant,p.Val147Met,ENST00000398907,;ERG,missense_variant,p.Val147Met,ENST00000398905,NM_001331025.2;ERG,missense_variant,p.Val55Met,ENST00000398897,NM_001243429.1;ERG,missense_variant,p.Val154Met,ENST00000398919,NM_001243428.1;ERG,missense_variant,p.Val55Met,ENST00000453032,NM_001136155.1;ERG,missense_variant,p.Val115Met,ENST00000429727,;ERG,non_coding_transcript_exon_variant,,ENST00000481609,;ERG,non_coding_transcript_exon_variant,,ENST00000492833,;ERG,non_coding_transcript_exon_variant,,ENST00000473107,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,; T ENSG00000157554 ENST00000417133 Transcript missense_variant 646/5023 460/1461 154/486 V/M Gtg/Atg 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS46648.1 ENSP00000414150 P11308.209 UPI000018681C NM_001243432.2,NM_001136154.1 deleterious(0.04) possibly_damaging(0.76) 6/12 Gene3D:1.10.150.50,PDB-ENSP_mappings:1sxe.A,Pfam:PF02198,PROSITE_profiles:PS51433,PANTHER:PTHR11849,PANTHER:PTHR11849:SF216,SMART:SM00251,Superfamily:SSF47769,CDD:cd08540 MODERATE 1 SNV 2 1 . ACC . . 38403659 -ERG 2078 . GRCh38 21 38575684 38575684 + Missense_Mutation SNP G G A rs201302788 TUMOR NORMAL G G c.17C>T p.Pro6Leu p.P6L ENST00000417133 3/12 191 92 99 0 . . ERG,missense_variant,p.Pro6Leu,ENST00000442448,NM_004449.4;ERG,missense_variant,p.Pro6Leu,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,missense_variant,p.Pro6Leu,ENST00000398910,NM_001291391.1;ERG,missense_variant,p.Pro6Leu,ENST00000398911,;ERG,missense_variant,p.Pro6Leu,ENST00000398919,NM_001243428.1;ERG,5_prime_UTR_variant,,ENST00000398897,NM_001243429.1;ERG,5_prime_UTR_variant,,ENST00000429727,;ERG,non_coding_transcript_exon_variant,,ENST00000485493,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,; A ENSG00000157554 ENST00000417133 Transcript missense_variant 203/5023 17/1461 6/486 P/L cCg/cTg rs201302788 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS46648.1 ENSP00000414150 P11308.209 UPI000018681C NM_001243432.2,NM_001136154.1 deleterious_low_confidence(0) benign(0.001) 3/12 0.0001163 MODERATE 1 SNV 2 1 . CGG . . 4.776e-05 0.0001056 38575684 -ERG 2078 . GRCh38 21 38575698 38575698 + Translation_Start_Site SNP C C T TUMOR NORMAL C C c.3G>A p.Met1? p.M1? ENST00000417133 3/12 331 223 96 449 442 0 ERG,start_lost,p.Met1?,ENST00000442448,NM_004449.4;ERG,start_lost,p.Met1?,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,start_lost,p.Met1?,ENST00000398910,NM_001291391.1;ERG,start_lost,p.Met1?,ENST00000398911,;ERG,start_lost,p.Met1?,ENST00000398919,NM_001243428.1;ERG,5_prime_UTR_variant,,ENST00000398897,NM_001243429.1;ERG,5_prime_UTR_variant,,ENST00000429727,;ERG,non_coding_transcript_exon_variant,,ENST00000485493,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,; T ENSG00000157554 ENST00000417133 Transcript start_lost 189/5023 3/1461 1/486 M/I atG/atA COSV67366082 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS46648.1 ENSP00000414150 P11308.209 UPI000018681C NM_001243432.2,NM_001136154.1 deleterious_low_confidence(0.03) benign(0.38) 3/12 1 HIGH 1 SNV 2 1 1 . TCA . . 38575698 -TMPRSS2 7113 . GRCh38 21 41479183 41479183 + Frame_Shift_Del DEL T T - novel TUMOR NORMAL T T c.831del p.Lys277AsnfsTer19 p.K277Nfs*19 ENST00000679263 7/14 512 435 77 695 695 0 TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000676973,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000679054,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000678348,;TMPRSS2,frameshift_variant,p.Lys277AsnfsTer19,ENST00000679263,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000332149,NM_005656.4;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000678171,NM_001382720.1;TMPRSS2,frameshift_variant,p.Lys155AsnfsTer19,ENST00000679016,;TMPRSS2,frameshift_variant,p.Lys261AsnfsTer19,ENST00000398585,NM_001135099.1;TMPRSS2,frameshift_variant,p.Lys116AsnfsTer19,ENST00000678743,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000454499,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000458356,;TMPRSS2,frameshift_variant,p.Lys184AsnfsTer19,ENST00000424093,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000678617,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000679181,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer16,ENST00000677680,;TMPRSS2,3_prime_UTR_variant,,ENST00000678959,;,regulatory_region_variant,,ENSR00001056496,; - ENSG00000184012 ENST00000679263 Transcript frameshift_variant 974/3623 831/1638 277/545 K/X aaA/aa 1 -1 TMPRSS2 HGNC HGNC:11876 protein_coding YES ENSP00000504602 7/14 Pfam:PF15494,Gene3D:3.10.250.10,SMART:SM00202,Superfamily:SSF56487,PANTHER:PTHR24253,PANTHER:PTHR24253:SF89 HIGH 1 deletion 1 . AGTT . . 41479182 -TMPRSS2 7113 . GRCh38 21 41479219 41479219 + Silent SNP C C T novel TUMOR NORMAL C C c.795G>A p.Leu265= p.L265= ENST00000679263 7/14 1224 782 373 1044 996 0 TMPRSS2,synonymous_variant,p.Leu212=,ENST00000676973,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000679054,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000678348,;TMPRSS2,synonymous_variant,p.Leu265=,ENST00000679263,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000332149,NM_005656.4;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000678171,NM_001382720.1;TMPRSS2,synonymous_variant,p.Leu143=,ENST00000679016,;TMPRSS2,synonymous_variant,p.Leu249=,ENST00000398585,NM_001135099.1;TMPRSS2,synonymous_variant,p.Leu104=,ENST00000678743,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000454499,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000458356,;TMPRSS2,synonymous_variant,p.Leu172=,ENST00000424093,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000678617,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000679181,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000677680,;TMPRSS2,3_prime_UTR_variant,,ENST00000678959,;,regulatory_region_variant,,ENSR00001056496,; T ENSG00000184012 ENST00000679263 Transcript synonymous_variant 938/3623 795/1638 265/545 L ctG/ctA 1 -1 TMPRSS2 HGNC HGNC:11876 protein_coding YES ENSP00000504602 7/14 Pfam:PF15494,Gene3D:3.10.250.10,SMART:SM00202,Superfamily:SSF56487,PANTHER:PTHR24253,PANTHER:PTHR24253:SF89 LOW 1 SNV 1 . TCA . . 41479219 -TMPRSS2 7113 . GRCh38 21 41488494 41488494 + Missense_Mutation SNP G G T TUMOR NORMAL G G c.504C>A p.Asn168Lys p.N168K ENST00000679263 5/14 380 350 30 0 . . TMPRSS2,missense_variant,p.Asn115Lys,ENST00000676973,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000679054,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000678348,;TMPRSS2,missense_variant,p.Asn168Lys,ENST00000679263,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000332149,NM_005656.4;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000678171,NM_001382720.1;TMPRSS2,missense_variant,p.Asn152Lys,ENST00000398585,NM_001135099.1;TMPRSS2,missense_variant,p.Asn7Lys,ENST00000678743,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000454499,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,;TMPRSS2,intron_variant,,ENST00000679016,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000678617,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000463138,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000679181,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000677680,;TMPRSS2,3_prime_UTR_variant,,ENST00000678959,; T ENSG00000184012 ENST00000679263 Transcript missense_variant 647/3623 504/1638 168/545 N/K aaC/aaA COSV59825472 1 -1 TMPRSS2 HGNC HGNC:11876 protein_coding YES ENSP00000504602 tolerated(0.95) benign(0.07) 5/14 CDD:cd00112,Gene3D:4.10.400.10,SMART:SM00192,Superfamily:SSF57424,PROSITE_profiles:PS50068,PANTHER:PTHR24253,PANTHER:PTHR24253:SF89 1 MODERATE 1 SNV 1 1 . AGT . . 41488494 -TMPRSS2 7113 . GRCh38 21 41494550 41494550 + Missense_Mutation SNP T T C rs774327563 TUMOR NORMAL T T c.203A>G p.Tyr68Cys p.Y68C ENST00000679263 3/14 356 260 96 781 781 0 TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000676973,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000679054,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000678348,;TMPRSS2,missense_variant,p.Tyr68Cys,ENST00000679263,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000332149,NM_005656.4;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000678171,NM_001382720.1;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000679016,;TMPRSS2,missense_variant,p.Tyr52Cys,ENST00000398585,NM_001135099.1;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000454499,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000458356,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000424093,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000455813,;TMPRSS2,intron_variant,,ENST00000678743,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000678617,;TMPRSS2,intron_variant,,ENST00000463138,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000679181,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000677680,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000678959,; C ENSG00000184012 ENST00000679263 Transcript missense_variant 346/3623 203/1638 68/545 Y/C tAt/tGt rs774327563 1 -1 TMPRSS2 HGNC HGNC:11876 protein_coding YES ENSP00000504602 tolerated(0.06) benign(0.412) 3/14 MODERATE 1 SNV 1 . ATA . . 1.995e-05 0.0001232 5.444e-05 1.762e-05 41494550 -UMODL1 89766 . GRCh38 21 42085325 42085325 + Silent SNP C C T rs185422923 TUMOR NORMAL C C c.516C>T p.Asn172= p.N172= ENST00000408989 4/22 366 193 173 0 . . UMODL1,synonymous_variant,p.Asn100=,ENST00000400424,NM_001199528.3;UMODL1,synonymous_variant,p.Asn100=,ENST00000400427,NM_001199527.2;UMODL1,synonymous_variant,p.Asn172=,ENST00000408989,NM_173568.3;UMODL1,synonymous_variant,p.Asn172=,ENST00000408910,NM_001004416.2;UMODL1,synonymous_variant,p.Asn8=,ENST00000491559,;UMODL1,synonymous_variant,p.Asn8=,ENST00000466434,;UMODL1,synonymous_variant,p.Asn8=,ENST00000400421,;UMODL1,synonymous_variant,p.Asn8=,ENST00000468982,;UMODL1,synonymous_variant,p.Asn8=,ENST00000485357,;UMODL1,synonymous_variant,p.Asn8=,ENST00000497243,; T ENSG00000177398 ENST00000408989 Transcript synonymous_variant 516/5262 516/4341 172/1446 N aaC/aaT rs185422923 1 1 UMODL1 HGNC HGNC:12560 protein_coding YES CCDS42935.1 ENSP00000386126 Q5DID0.131 UPI0000D6254B NM_173568.3 4/22 PANTHER:PTHR14002,PANTHER:PTHR14002:SF22 0.0002 0.0008 0.0001207 LOW 1 SNV 1 . ACG . . 8.016e-06 6.457e-05 3.268e-05 42085325 -U2AF1 7307 . GRCh38 21 43093128 43093128 + Missense_Mutation SNP C C T novel TUMOR NORMAL C C c.697G>A p.Asp233Asn p.D233N ENST00000291552 8/8 454 425 29 344 344 0 U2AF1,missense_variant,p.Asp160Asn,ENST00000459639,NM_001025204.1;U2AF1,missense_variant,p.Asp233Asn,ENST00000291552,NM_006758.3;U2AF1,missense_variant,p.Asp233Asn,ENST00000380276,NM_001025203.1;U2AF1,3_prime_UTR_variant,,ENST00000464750,;U2AF1,non_coding_transcript_exon_variant,,ENST00000475639,;U2AF1,non_coding_transcript_exon_variant,,ENST00000478282,;U2AF1,non_coding_transcript_exon_variant,,ENST00000471250,;U2AF1,downstream_gene_variant,,ENST00000463599,;U2AF1,downstream_gene_variant,,ENST00000486519,;U2AF1,downstream_gene_variant,,ENST00000496462,; T ENSG00000160201 ENST00000291552 Transcript missense_variant 773/945 697/723 233/240 D/N Gat/Aat 1 -1 U2AF1 HGNC HGNC:12453 protein_coding YES CCDS13694.1 ENSP00000291552 Q01081.224 UPI0000000C26 NM_006758.3 tolerated(0.44) possibly_damaging(0.857) 8/8 PANTHER:PTHR12620,PANTHER:PTHR12620:SF11,MobiDB_lite:mobidb-lite,MobiDB_lite:mobidb-lite,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 . TCT . . 43093128 -U2AF1 7307 . GRCh38 21 43104375 43104375 + Silent SNP A A G rs755067307 TUMOR NORMAL A A c.72T>C p.Ile24= p.I24= ENST00000291552 2/8 667 607 60 0 . . U2AF1,synonymous_variant,p.Ile24=,ENST00000291552,NM_006758.3;U2AF1,synonymous_variant,p.Ile24=,ENST00000380276,NM_001025203.1;U2AF1,5_prime_UTR_variant,,ENST00000459639,NM_001025204.1;AP001631.2,upstream_gene_variant,,ENST00000668861,;U2AF1,synonymous_variant,p.Ile24=,ENST00000464750,;U2AF1,synonymous_variant,p.Ile24=,ENST00000486519,;U2AF1,non_coding_transcript_exon_variant,,ENST00000475639,;U2AF1,non_coding_transcript_exon_variant,,ENST00000496462,;U2AF1,non_coding_transcript_exon_variant,,ENST00000463599,;U2AF1,upstream_gene_variant,,ENST00000468039,; G ENSG00000160201 ENST00000291552 Transcript synonymous_variant 148/945 72/723 24/240 I atT/atC rs755067307 1 -1 U2AF1 HGNC HGNC:12453 protein_coding YES CCDS13694.1 ENSP00000291552 Q01081.224 UPI0000000C26 NM_006758.3 2/8 Pfam:PF00642,Prints:PR01848,PROSITE_profiles:PS50103,PANTHER:PTHR12620,PANTHER:PTHR12620:SF11,SMART:SM00356 LOW 1 SNV 1 1 . CAA . . 7.992e-06 2.921e-05 8.823e-06 43104375 -SIK1 150094 . GRCh38 21 43419117 43419117 + Missense_Mutation SNP C C T novel TUMOR NORMAL C C c.1366G>A p.Glu456Lys p.E456K ENST00000270162 11/14 113 . 45 0 . . SIK1,missense_variant,p.Glu456Lys,ENST00000270162,NM_173354.5;SIK1,downstream_gene_variant,,ENST00000644750,;SIK1,downstream_gene_variant,,ENST00000478426,;SIK1,downstream_gene_variant,,ENST00000644689,;SIK1,downstream_gene_variant,,ENST00000644871,; T ENSG00000142178 ENST00000270162 Transcript missense_variant 1502/4747 1366/2352 456/783 E/K Gag/Aag 1 -1 SIK1 HGNC HGNC:11142 protein_coding YES CCDS33575.1 ENSP00000270162 P57059.191 UPI0000206F2B NM_173354.5 deleterious(0.03) possibly_damaging(0.494) 11/14 PIRSF:PIRSF037014,PANTHER:PTHR24346,PANTHER:PTHR24346:SF47,MobiDB_lite:mobidb-lite MODERATE 1 SNV 1 1 . TCC . . 43419117 -ICOSLG 23308 . GRCh38 21 44235374 44235374 + Missense_Mutation SNP C C A TUMOR NORMAL C C c.595G>T p.Val199Leu p.V199L ENST00000400379 4/6 101 88 13 153 153 0 ICOSLG,missense_variant,p.Val199Leu,ENST00000407780,NM_001283052.2,NM_015259.6,NM_001365759.2;ICOSLG,missense_variant,p.Val199Leu,ENST00000400379,;ICOSLG,missense_variant,p.Val82Leu,ENST00000400377,NM_001283051.2;ICOSLG,missense_variant,p.Val199Leu,ENST00000344330,NM_001283050.2; A ENSG00000160223 ENST00000400379 Transcript missense_variant 723/4246 595/1422 199/473 V/L Gtg/Ttg COSV60266097 1 -1 ICOSLG HGNC HGNC:17087 protein_coding YES ENSP00000383230 K4DIA0.68 UPI00003E5A05 tolerated(0.06) probably_damaging(0.982) 4/6 Superfamily:SSF48726,Gene3D:2.60.40.10,PANTHER:PTHR24100,PANTHER:PTHR24100:SF55,PROSITE_profiles:PS50835 1 MODERATE 1 SNV 1 1 . ACG . . 44235374 -ICOSLG 23308 . GRCh38 21 44236903 44236903 + Missense_Mutation SNP C C T novel TUMOR NORMAL C C c.370G>A p.Glu124Lys p.E124K ENST00000400379 3/6 950 827 123 630 629 1 ICOSLG,missense_variant,p.Glu124Lys,ENST00000407780,NM_001283052.2,NM_015259.6,NM_001365759.2;ICOSLG,missense_variant,p.Glu124Lys,ENST00000400379,;ICOSLG,missense_variant,p.Glu124Lys,ENST00000344330,NM_001283050.2;ICOSLG,intron_variant,,ENST00000400377,NM_001283051.2;AP001059.2,upstream_gene_variant,,ENST00000619053,; T ENSG00000160223 ENST00000400379 Transcript missense_variant 498/4246 370/1422 124/473 E/K Gag/Aag 1 -1 ICOSLG HGNC HGNC:17087 protein_coding YES ENSP00000383230 K4DIA0.68 UPI00003E5A05 tolerated(0.37) benign(0.031) 3/6 Superfamily:SSF48726,SMART:SM00409,Pfam:PF07686,Gene3D:2.60.40.10,PANTHER:PTHR24100,PANTHER:PTHR24100:SF55,PROSITE_profiles:PS50835 MODERATE 1 SNV 1 . TCC . . 44236903 -ICOSLG 23308 . GRCh38 21 44237111 44237111 + Nonsense_Mutation SNP C C T novel TUMOR NORMAL C C c.162G>A p.Trp54Ter p.W54* ENST00000400379 3/6 944 745 199 596 596 0 ICOSLG,stop_gained,p.Trp54Ter,ENST00000407780,NM_001283052.2,NM_015259.6,NM_001365759.2;ICOSLG,stop_gained,p.Trp54Ter,ENST00000400379,;ICOSLG,stop_gained,p.Trp54Ter,ENST00000344330,NM_001283050.2;ICOSLG,intron_variant,,ENST00000400377,NM_001283051.2;AP001059.2,upstream_gene_variant,,ENST00000619053,; T ENSG00000160223 ENST00000400379 Transcript stop_gained 290/4246 162/1422 54/473 W/* tgG/tgA 1 -1 ICOSLG HGNC HGNC:17087 protein_coding YES ENSP00000383230 K4DIA0.68 UPI00003E5A05 3/6 Superfamily:SSF48726,SMART:SM00409,Pfam:PF07686,Gene3D:2.60.40.10,PANTHER:PTHR24100,PANTHER:PTHR24100:SF55,PROSITE_profiles:PS50835 HIGH 1 SNV 1 . GCC . . 44237111 +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND_VEP SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS AF AFR_AF AMR_AF ASN_AF EAS_AF EUR_AF SAS_AF AA_AF EA_AF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO MINIMISED GENE_PHENO FILTER flanking_bps vcf_id vcf_qual gnomADe_AF gnomADe_AFR_AF gnomADe_AMR_AF gnomADe_ASJ_AF gnomADe_EAS_AF gnomADe_FIN_AF gnomADe_NFE_AF gnomADe_OTH_AF gnomADe_SAS_AF vcf_pos +RUNX1 861 . GRCh38 21 34792292 34792292 + Missense_Mutation SNP A A C rs2056450952 TUMOR NORMAL A A c.1286T>G p.Leu429Arg p.L429R ENST00000675419 9/9 54 . 21 0 . . RUNX1,missense_variant,p.Leu402Arg,ENST00000344691,NM_001001890.3;RUNX1,missense_variant,p.Leu429Arg,ENST00000300305,;RUNX1,missense_variant,p.Leu429Arg,ENST00000675419,NM_001754.5;RUNX1,missense_variant,p.Leu338Arg,ENST00000399240,;RUNX1,3_prime_UTR_variant,,ENST00000482318,; C ENSG00000159216 ENST00000675419 Transcript missense_variant 1480/5971 1286/1443 429/480 L/R cTg/cGg rs2056450952 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000501943 Q01196.255 UPI000015FE6A NM_001754.5 deleterious_low_confidence(0) 9/9 AlphaFold_DB_import:AF-Q01196-F1,Pfam:PF08504,PIRSF:PIRSF009374,Prints:PR00967,PANTHER:PTHR11950 uncertain_significance MODERATE 1 SNV 1 1 . CAG . . 34792292 +RUNX1 861 . GRCh38 21 34792478 34792478 + Missense_Mutation SNP C C T rs867474432 TUMOR NORMAL C C c.1100G>A p.Gly367Asp p.G367D ENST00000675419 9/9 901 778 123 482 482 0 RUNX1,missense_variant,p.Gly340Asp,ENST00000344691,NM_001001890.3;RUNX1,missense_variant,p.Gly367Asp,ENST00000300305,;RUNX1,missense_variant,p.Gly367Asp,ENST00000675419,NM_001754.5;RUNX1,missense_variant,p.Gly276Asp,ENST00000399240,;RUNX1,3_prime_UTR_variant,,ENST00000482318,; T ENSG00000159216 ENST00000675419 Transcript missense_variant 1294/5971 1100/1443 367/480 G/D gGc/gAc rs867474432,COSV55867253 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000501943 Q01196.255 UPI000015FE6A NM_001754.5 deleterious_low_confidence(0.01) 9/9 Gene3D:4.10.770.10,AlphaFold_DB_import:AF-Q01196-F1,PIRSF:PIRSF009374,PANTHER:PTHR11950,Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 0,1 1 . GCC . . 34792478 +RUNX1 861 . GRCh38 21 34880549 34880549 + Splice_Region SNP T T C novel TUMOR NORMAL T T c.508+8A>G ENST00000675419 504 450 54 0 . . RUNX1,splice_region_variant,,ENST00000300305,;RUNX1,splice_region_variant,,ENST00000344691,NM_001001890.3;RUNX1,splice_region_variant,,ENST00000358356,NM_001122607.2;RUNX1,splice_region_variant,,ENST00000399237,;RUNX1,splice_region_variant,,ENST00000399240,;RUNX1,splice_region_variant,,ENST00000675419,NM_001754.5;RUNX1,downstream_gene_variant,,ENST00000455571,;RUNX1-AS1,intron_variant,,ENST00000651798,;RUNX1,splice_region_variant,,ENST00000482318,;,regulatory_region_variant,,ENSR00001365449,; C ENSG00000159216 ENST00000675419 Transcript splice_region_variant,intron_variant 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000501943 Q01196.255 UPI000015FE6A NM_001754.5 5/8 LOW 1 SNV 1 . ATA . . 34880549 +RUNX1 861 . GRCh38 21 34880555 34880556 + Splice_Site INS - - CCTCTT novel TUMOR NORMAL - - c.504_508+1dup p.X168_splice ENST00000675419 883 658 225 343 343 0 RUNX1,splice_donor_variant,,ENST00000300305,;RUNX1,splice_donor_variant,,ENST00000344691,NM_001001890.3;RUNX1,splice_donor_variant,,ENST00000358356,NM_001122607.2;RUNX1,splice_donor_variant,,ENST00000399237,;RUNX1,splice_donor_variant,,ENST00000399240,;RUNX1,splice_donor_variant,,ENST00000675419,NM_001754.5;RUNX1,downstream_gene_variant,,ENST00000455571,;RUNX1-AS1,intron_variant,,ENST00000651798,;RUNX1,splice_donor_variant,,ENST00000482318,;,regulatory_region_variant,,ENSR00001365449,; CCTCTT ENSG00000159216 ENST00000675419 Transcript splice_donor_variant 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000501943 Q01196.255 UPI000015FE6A NM_001754.5 5/8 HIGH 1 insertion 1 . TAC . . 34880555 +RUNX1 861 . GRCh38 21 34880595 34880595 + Missense_Mutation SNP C C T rs2146361175 TUMOR NORMAL C C c.470G>A p.Arg157Lys p.R157K ENST00000675419 5/9 862 788 74 523 522 1 RUNX1,missense_variant,p.Arg130Lys,ENST00000344691,NM_001001890.3;RUNX1,missense_variant,p.Arg157Lys,ENST00000300305,;RUNX1,missense_variant,p.Arg157Lys,ENST00000675419,NM_001754.5;RUNX1,missense_variant,p.Arg130Lys,ENST00000358356,NM_001122607.2;RUNX1,missense_variant,p.Arg130Lys,ENST00000399240,;RUNX1,missense_variant,p.Arg145Lys,ENST00000399237,;RUNX1,downstream_gene_variant,,ENST00000455571,;RUNX1-AS1,intron_variant,,ENST00000651798,;RUNX1,3_prime_UTR_variant,,ENST00000482318,;,regulatory_region_variant,,ENSR00001365449,; T ENSG00000159216 ENST00000675419 Transcript missense_variant 664/5971 470/1443 157/480 R/K aGa/aAa rs2146361175,COSV55871984,COSV55885034 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000501943 Q01196.255 UPI000015FE6A NM_001754.5 deleterious_low_confidence(0.01) 5/9 Gene3D:2.60.40.720,AlphaFold_DB_import:AF-Q01196-F1,Pfam:PF00853,PIRSF:PIRSF009374,Prints:PR00967,PROSITE_profiles:PS51062,PANTHER:PTHR11950,Superfamily:SSF49417 0,1,1 MODERATE 1 SNV 0,1,1 1 . TCT . . 34880595 +RUNX1 861 . GRCh38 21 34880650 34880651 + Frame_Shift_Ins INS - - G novel TUMOR NORMAL - - c.414_415insC p.Asn139GlnfsTer5 p.N139Qfs*5 ENST00000675419 5/9 611 449 162 528 527 1 RUNX1,frameshift_variant,p.Asn112GlnfsTer5,ENST00000344691,NM_001001890.3;RUNX1,frameshift_variant,p.Asn139GlnfsTer5,ENST00000300305,;RUNX1,frameshift_variant,p.Asn139GlnfsTer5,ENST00000675419,NM_001754.5;RUNX1,frameshift_variant,p.Asn112GlnfsTer5,ENST00000358356,NM_001122607.2;RUNX1,frameshift_variant,p.Asn112GlnfsTer5,ENST00000399240,;RUNX1,frameshift_variant,p.Asn127GlnfsTer5,ENST00000399237,;RUNX1,frameshift_variant,p.Asn126GlnfsTer5,ENST00000455571,;RUNX1-AS1,intron_variant,,ENST00000651798,;RUNX1,3_prime_UTR_variant,,ENST00000482318,;,regulatory_region_variant,,ENSR00001365449,; G ENSG00000159216 ENST00000675419 Transcript frameshift_variant 608-609/5971 414-415/1443 138-139/480 -/X -/C 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000501943 Q01196.255 UPI000015FE6A NM_001754.5 5/9 Gene3D:2.60.40.720,AlphaFold_DB_import:AF-Q01196-F1,Pfam:PF00853,PIRSF:PIRSF009374,Prints:PR00967,PROSITE_profiles:PS51062,PANTHER:PTHR11950,Superfamily:SSF49417 HIGH 1 insertion 1 . TTT . . 34880650 +RUNX1 861 . GRCh38 21 34886911 34886911 + Missense_Mutation SNP G G A rs2057999086 TUMOR NORMAL G G c.283C>T p.Pro95Ser p.P95S ENST00000675419 4/9 51 34 17 0 . . RUNX1,missense_variant,p.Pro68Ser,ENST00000344691,NM_001001890.3;RUNX1,missense_variant,p.Pro95Ser,ENST00000300305,;RUNX1,missense_variant,p.Pro95Ser,ENST00000675419,NM_001754.5;RUNX1,missense_variant,p.Pro68Ser,ENST00000358356,NM_001122607.2;RUNX1,missense_variant,p.Pro68Ser,ENST00000399240,;RUNX1,missense_variant,p.Pro83Ser,ENST00000399237,;RUNX1,missense_variant,p.Pro82Ser,ENST00000455571,;RUNX1,downstream_gene_variant,,ENST00000475045,;RUNX1-AS1,downstream_gene_variant,,ENST00000651798,;RUNX1,intron_variant,,ENST00000482318,;,regulatory_region_variant,,ENSR00001365449,; A ENSG00000159216 ENST00000675419 Transcript missense_variant 477/5971 283/1443 95/480 P/S Ccc/Tcc rs2057999086 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000501943 Q01196.255 UPI000015FE6A NM_001754.5 deleterious_low_confidence(0.01) 4/9 Gene3D:2.60.40.720,AlphaFold_DB_import:AF-Q01196-F1,Pfam:PF00853,PIRSF:PIRSF009374,Prints:PR00967,Prints:PR00967,PROSITE_profiles:PS51062,PANTHER:PTHR11950,Superfamily:SSF49417 uncertain_significance MODERATE 1 SNV 1 1 . GGG . . 34886911 +SETD4 54093 . GRCh38 21 36043782 36043782 + Missense_Mutation SNP C C G novel TUMOR NORMAL C C c.901G>C p.Glu301Gln p.E301Q ENST00000332131 7/12 1140 1010 130 975 975 0 SETD4,missense_variant,p.Glu301Gln,ENST00000399215,;SETD4,missense_variant,p.Glu277Gln,ENST00000399212,NM_001286752.2;SETD4,missense_variant,p.Glu301Gln,ENST00000332131,NM_017438.5;SETD4,missense_variant,p.Gly277Arg,ENST00000399201,;SETD4,missense_variant,p.Gly277Arg,ENST00000399205,NM_001007261.3;SETD4,missense_variant,p.Gly301Arg,ENST00000399208,NM_001007259.3;SETD4,missense_variant,p.Gly301Arg,ENST00000399207,;SETD4,downstream_gene_variant,,ENST00000424303,;SETD4,downstream_gene_variant,,ENST00000429161,;SETD4,downstream_gene_variant,,ENST00000442559,;SETD4,downstream_gene_variant,,ENST00000446166,;SETD4,splice_region_variant,,ENST00000481477,;SETD4,upstream_gene_variant,,ENST00000469482,;SETD4,downstream_gene_variant,,ENST00000485865,;SETD4,upstream_gene_variant,,ENST00000487297,; G ENSG00000185917 ENST00000332131 Transcript missense_variant,splice_region_variant 1117/2991 901/1323 301/440 E/Q Gaa/Caa 1 -1 SETD4 HGNC HGNC:1258 protein_coding YES CCDS13640.1 ENSP00000329189 Q9NVD3.174 UPI000012868E NM_017438.5 deleterious(0) benign(0.21) 7/12 PANTHER:PTHR13271,PIRSF:PIRSF027158,AlphaFold_DB_import:AF-Q9NVD3-F1 MODERATE 1 SNV 2 . CCT . . 36043782 +ERG 2078 . GRCh38 21 38383625 38383625 + Silent SNP T T C novel TUMOR NORMAL T T c.1218A>G p.Ser406= p.S406= ENST00000288319 10/10 352 329 23 0 . . ERG,synonymous_variant,p.Ser389=,ENST00000442448,NM_004449.4;ERG,synonymous_variant,p.Ser413=,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,synonymous_variant,p.Ser390=,ENST00000398910,NM_001291391.1;ERG,synonymous_variant,p.Ser389=,ENST00000398911,;ERG,synonymous_variant,p.Ser406=,ENST00000288319,NM_182918.4;ERG,synonymous_variant,p.Ser383=,ENST00000398907,;ERG,synonymous_variant,p.Ser382=,ENST00000398905,NM_001331025.2;ERG,synonymous_variant,p.Ser290=,ENST00000398897,NM_001243429.1;ERG,synonymous_variant,p.Ser413=,ENST00000398919,NM_001243428.1;ERG,synonymous_variant,p.Ser314=,ENST00000453032,NM_001136155.1; C ENSG00000157554 ENST00000288319 Transcript synonymous_variant 1315/4904 1218/1440 406/479 S tcA/tcG 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS13658.1 ENSP00000288319 P11308.226 UPI0000074389 NM_182918.4 10/10 PDB-ENSP_mappings:6vge.A,PDB-ENSP_mappings:6vgg.A,AlphaFold_DB_import:AF-P11308-F1,Superfamily:SSF46785 LOW 1 SNV 1 1 . ATG . . 38383625 +ERG 2078 . GRCh38 21 38400597 38400597 + Missense_Mutation SNP G G A rs1988442233 TUMOR NORMAL G G c.722C>T p.Thr241Met p.T241M ENST00000288319 6/10 1199 892 307 567 566 1 ERG,missense_variant,p.Thr248Met,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,missense_variant,p.Thr248Met,ENST00000398910,NM_001291391.1;ERG,missense_variant,p.Thr241Met,ENST00000288319,NM_182918.4;ERG,missense_variant,p.Thr241Met,ENST00000398907,;ERG,missense_variant,p.Thr248Met,ENST00000398919,NM_001243428.1;ERG,missense_variant,p.Thr149Met,ENST00000453032,NM_001136155.1;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398905,NM_001331025.2;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,non_coding_transcript_exon_variant,,ENST00000492833,;ERG,intron_variant,,ENST00000481609,;ERG,downstream_gene_variant,,ENST00000473107,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,;,regulatory_region_variant,,ENSR00000662899,; A ENSG00000157554 ENST00000288319 Transcript missense_variant 819/4904 722/1440 241/479 T/M aCg/aTg rs1988442233,COSV55741264 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS13658.1 ENSP00000288319 P11308.226 UPI0000074389 NM_182918.4 tolerated(0.11) 6/10 AlphaFold_DB_import:AF-P11308-F1,PANTHER:PTHR11849 0,1 MODERATE 1 SNV 1 0,1 1 . CGT . . 38400597 +ERG 2078 . GRCh38 21 38400606 38400606 + Missense_Mutation SNP G G T TUMOR NORMAL G G c.713C>A p.Pro238His p.P238H ENST00000288319 6/10 343 190 153 507 507 0 ERG,missense_variant,p.Pro245His,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,missense_variant,p.Pro245His,ENST00000398910,NM_001291391.1;ERG,missense_variant,p.Pro238His,ENST00000288319,NM_182918.4;ERG,missense_variant,p.Pro238His,ENST00000398907,;ERG,missense_variant,p.Pro245His,ENST00000398919,NM_001243428.1;ERG,missense_variant,p.Pro146His,ENST00000453032,NM_001136155.1;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398905,NM_001331025.2;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,non_coding_transcript_exon_variant,,ENST00000492833,;ERG,intron_variant,,ENST00000481609,;ERG,downstream_gene_variant,,ENST00000473107,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,;,regulatory_region_variant,,ENSR00000662899,; T ENSG00000157554 ENST00000288319 Transcript missense_variant 810/4904 713/1440 238/479 P/H cCt/cAt COSV55741651 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS13658.1 ENSP00000288319 P11308.226 UPI0000074389 NM_182918.4 deleterious(0.04) 6/10 AlphaFold_DB_import:AF-P11308-F1,PANTHER:PTHR11849 1 MODERATE 1 SNV 1 1 1 . AGG . . 38400606 +ERG 2078 . GRCh38 21 38403659 38403659 + Missense_Mutation SNP C C T rs1988621553 TUMOR NORMAL C C c.439G>A p.Val147Met p.V147M ENST00000288319 4/10 287 149 138 0 . . ERG,missense_variant,p.Val154Met,ENST00000442448,NM_004449.4;ERG,missense_variant,p.Val154Met,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,missense_variant,p.Val154Met,ENST00000398910,NM_001291391.1;ERG,missense_variant,p.Val154Met,ENST00000398911,;ERG,missense_variant,p.Val147Met,ENST00000288319,NM_182918.4;ERG,missense_variant,p.Val147Met,ENST00000398907,;ERG,missense_variant,p.Val147Met,ENST00000398905,NM_001331025.2;ERG,missense_variant,p.Val55Met,ENST00000398897,NM_001243429.1;ERG,missense_variant,p.Val154Met,ENST00000398919,NM_001243428.1;ERG,missense_variant,p.Val55Met,ENST00000453032,NM_001136155.1;ERG,non_coding_transcript_exon_variant,,ENST00000481609,;ERG,non_coding_transcript_exon_variant,,ENST00000492833,;ERG,non_coding_transcript_exon_variant,,ENST00000473107,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,; T ENSG00000157554 ENST00000288319 Transcript missense_variant 536/4904 439/1440 147/479 V/M Gtg/Atg rs1988621553 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS13658.1 ENSP00000288319 P11308.226 UPI0000074389 NM_182918.4 deleterious(0.02) 4/10 Gene3D:1.10.150.50,PDB-ENSP_mappings:1sxe.A,AlphaFold_DB_import:AF-P11308-F1,Pfam:PF02198,PROSITE_profiles:PS51433,PANTHER:PTHR11849,SMART:SM00251,Superfamily:SSF47769,CDD:cd08540 MODERATE 1 SNV 1 1 . ACC . . 38403659 +ERG 2078 . GRCh38 21 38575684 38575684 + Missense_Mutation SNP G G A rs201302788 TUMOR NORMAL G G c.17C>T p.Pro6Leu p.P6L ENST00000442448 3/11 191 92 99 0 . . ERG,missense_variant,p.Pro6Leu,ENST00000442448,NM_004449.4;ERG,missense_variant,p.Pro6Leu,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,missense_variant,p.Pro6Leu,ENST00000398910,NM_001291391.1;ERG,missense_variant,p.Pro6Leu,ENST00000398911,;ERG,missense_variant,p.Pro6Leu,ENST00000398919,NM_001243428.1;ERG,5_prime_UTR_variant,,ENST00000398897,NM_001243429.1;ERG,non_coding_transcript_exon_variant,,ENST00000485493,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,; A ENSG00000157554 ENST00000442448 Transcript missense_variant 289/5034 17/1389 6/462 P/L cCg/cTg rs201302788 1 -1 ERG HGNC HGNC:3446 protein_coding CCDS13657.1 ENSP00000394694 P11308.226 UPI0000046820 NM_004449.4 deleterious_low_confidence(0.01) benign(0.005) 3/11 AlphaFold_DB_import:AF-P11308-F1 MODERATE SNV 5 1 . CGG . . 4.776e-05 0.0001056 38575684 +ERG 2078 . GRCh38 21 38575698 38575698 + Translation_Start_Site SNP C C T TUMOR NORMAL C C c.3G>A p.Met1? p.M1? ENST00000442448 3/11 331 223 96 449 442 0 ERG,start_lost,p.Met1?,ENST00000442448,NM_004449.4;ERG,start_lost,p.Met1?,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,start_lost,p.Met1?,ENST00000398910,NM_001291391.1;ERG,start_lost,p.Met1?,ENST00000398911,;ERG,start_lost,p.Met1?,ENST00000398919,NM_001243428.1;ERG,5_prime_UTR_variant,,ENST00000398897,NM_001243429.1;ERG,non_coding_transcript_exon_variant,,ENST00000485493,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,; T ENSG00000157554 ENST00000442448 Transcript start_lost 275/5034 3/1389 1/462 M/I atG/atA COSV67366082 1 -1 ERG HGNC HGNC:3446 protein_coding CCDS13657.1 ENSP00000394694 P11308.226 UPI0000046820 NM_004449.4 deleterious_low_confidence(0.01) benign(0.223) 3/11 AlphaFold_DB_import:AF-P11308-F1 1 HIGH SNV 5 1 1 . TCA . . 38575698 +TMPRSS2 7113 . GRCh38 21 41479183 41479183 + Frame_Shift_Del DEL T T - novel TUMOR NORMAL T T c.672del p.Lys224AsnfsTer19 p.K224Nfs*19 ENST00000332149 7/14 512 435 77 695 695 0 TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000676973,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000679054,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000678348,;TMPRSS2,frameshift_variant,p.Lys277AsnfsTer19,ENST00000679263,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000332149,NM_005656.4;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000678171,NM_001382720.1;TMPRSS2,frameshift_variant,p.Lys155AsnfsTer19,ENST00000679016,;TMPRSS2,frameshift_variant,p.Lys261AsnfsTer19,ENST00000398585,NM_001135099.1;TMPRSS2,frameshift_variant,p.Lys116AsnfsTer19,ENST00000678743,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000454499,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000458356,;TMPRSS2,frameshift_variant,p.Lys184AsnfsTer19,ENST00000424093,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000678617,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000679181,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer16,ENST00000677680,;TMPRSS2,3_prime_UTR_variant,,ENST00000678959,; - ENSG00000184012 ENST00000332149 Transcript frameshift_variant 806/3450 672/1479 224/492 K/X aaA/aa 1 -1 TMPRSS2 HGNC HGNC:11876 protein_coding YES CCDS33564.1 ENSP00000330330 O15393.205 UPI0000049921 NM_005656.4 7/14 PDB-ENSP_mappings:7meq.A,Pfam:PF15494,Gene3D:3.10.250.10,SMART:SM00202,Superfamily:SSF56487,PANTHER:PTHR24253,AlphaFold_DB_import:AF-O15393-F1 HIGH 1 deletion 1 1 . AGTT . . 41479182 +TMPRSS2 7113 . GRCh38 21 41479219 41479219 + Silent SNP C C T TUMOR NORMAL C C c.636G>A p.Leu212= p.L212= ENST00000332149 7/14 1224 782 373 1044 996 0 TMPRSS2,synonymous_variant,p.Leu212=,ENST00000676973,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000679054,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000678348,;TMPRSS2,synonymous_variant,p.Leu265=,ENST00000679263,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000332149,NM_005656.4;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000678171,NM_001382720.1;TMPRSS2,synonymous_variant,p.Leu143=,ENST00000679016,;TMPRSS2,synonymous_variant,p.Leu249=,ENST00000398585,NM_001135099.1;TMPRSS2,synonymous_variant,p.Leu104=,ENST00000678743,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000454499,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000458356,;TMPRSS2,synonymous_variant,p.Leu172=,ENST00000424093,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000678617,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000679181,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000677680,;TMPRSS2,3_prime_UTR_variant,,ENST00000678959,; T ENSG00000184012 ENST00000332149 Transcript synonymous_variant 770/3450 636/1479 212/492 L ctG/ctA COSV106461584 1 -1 TMPRSS2 HGNC HGNC:11876 protein_coding YES CCDS33564.1 ENSP00000330330 O15393.205 UPI0000049921 NM_005656.4 7/14 PDB-ENSP_mappings:7meq.A,Pfam:PF15494,Gene3D:3.10.250.10,SMART:SM00202,Superfamily:SSF56487,PANTHER:PTHR24253,AlphaFold_DB_import:AF-O15393-F1 1 LOW 1 SNV 1 1 1 . TCA . . 41479219 +TMPRSS2 7113 . GRCh38 21 41488494 41488494 + Missense_Mutation SNP G G T TUMOR NORMAL G G c.345C>A p.Asn115Lys p.N115K ENST00000332149 5/14 380 350 30 0 . . TMPRSS2,missense_variant,p.Asn115Lys,ENST00000676973,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000679054,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000678348,;TMPRSS2,missense_variant,p.Asn168Lys,ENST00000679263,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000332149,NM_005656.4;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000678171,NM_001382720.1;TMPRSS2,missense_variant,p.Asn152Lys,ENST00000398585,NM_001135099.1;TMPRSS2,missense_variant,p.Asn7Lys,ENST00000678743,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000454499,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,;TMPRSS2,intron_variant,,ENST00000679016,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000678617,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000463138,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000679181,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000677680,;TMPRSS2,3_prime_UTR_variant,,ENST00000678959,; T ENSG00000184012 ENST00000332149 Transcript missense_variant 479/3450 345/1479 115/492 N/K aaC/aaA COSV59825472 1 -1 TMPRSS2 HGNC HGNC:11876 protein_coding YES CCDS33564.1 ENSP00000330330 O15393.205 UPI0000049921 NM_005656.4 tolerated(0.84) benign(0.013) 5/14 PDB-ENSP_mappings:7meq.A,CDD:cd00112,Gene3D:4.10.400.10,SMART:SM00192,Superfamily:SSF57424,PROSITE_profiles:PS50068,AlphaFold_DB_import:AF-O15393-F1 1 MODERATE 1 SNV 1 1 1 . AGT . . 41488494 +TMPRSS2 7113 . GRCh38 21 41494550 41494550 + Missense_Mutation SNP T T C rs774327563 TUMOR NORMAL T T c.44A>G p.Tyr15Cys p.Y15C ENST00000332149 3/14 356 260 96 781 781 0 TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000676973,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000679054,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000678348,;TMPRSS2,missense_variant,p.Tyr68Cys,ENST00000679263,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000332149,NM_005656.4;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000678171,NM_001382720.1;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000679016,;TMPRSS2,missense_variant,p.Tyr52Cys,ENST00000398585,NM_001135099.1;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000454499,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000458356,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000424093,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000455813,;TMPRSS2,intron_variant,,ENST00000678743,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000678617,;TMPRSS2,intron_variant,,ENST00000463138,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000679181,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000677680,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000678959,; C ENSG00000184012 ENST00000332149 Transcript missense_variant 178/3450 44/1479 15/492 Y/C tAt/tGt rs774327563 1 -1 TMPRSS2 HGNC HGNC:11876 protein_coding YES CCDS33564.1 ENSP00000330330 O15393.205 UPI0000049921 NM_005656.4 deleterious(0.01) benign(0.022) 3/14 AlphaFold_DB_import:AF-O15393-F1 MODERATE 1 SNV 1 1 . ATA . . 1.995e-05 0.0001232 5.444e-05 1.762e-05 41494550 +UMODL1 89766 . GRCh38 21 42085325 42085325 + Silent SNP C C T rs185422923 TUMOR NORMAL C C c.516C>T p.Asn172= p.N172= ENST00000408910 4/23 366 193 173 0 . . UMODL1,synonymous_variant,p.Asn100=,ENST00000400424,NM_001199528.4;UMODL1,synonymous_variant,p.Asn100=,ENST00000400427,NM_001199527.3;UMODL1,synonymous_variant,p.Asn172=,ENST00000408989,NM_173568.4;UMODL1,synonymous_variant,p.Asn172=,ENST00000408910,NM_001004416.3;UMODL1,synonymous_variant,p.Asn8=,ENST00000491559,;UMODL1,synonymous_variant,p.Asn8=,ENST00000466434,;UMODL1,synonymous_variant,p.Asn8=,ENST00000400421,;UMODL1,synonymous_variant,p.Asn8=,ENST00000468982,;UMODL1,synonymous_variant,p.Asn8=,ENST00000485357,;UMODL1,synonymous_variant,p.Asn8=,ENST00000497243,; T ENSG00000177398 ENST00000408910 Transcript synonymous_variant 516/4879 516/3957 172/1318 N aaC/aaT rs185422923 1 1 UMODL1 HGNC HGNC:12560 protein_coding YES CCDS42936.1 ENSP00000386147 Q5DID0.147 UPI00006C2192 NM_001004416.3 4/23 AlphaFold_DB_import:AF-Q5DID0-F1 0.0002 0.0008 LOW 1 SNV 1 . ACG . . 8.016e-06 6.457e-05 3.268e-05 42085325 +U2AF1 7307 . GRCh38 21 43093128 43093128 + Missense_Mutation SNP C C T novel TUMOR NORMAL C C c.697G>A p.Asp233Asn p.D233N ENST00000291552 8/8 454 425 29 344 344 0 U2AF1,missense_variant,p.Asp160Asn,ENST00000459639,NM_001025204.2;U2AF1,missense_variant,p.Asp233Asn,ENST00000291552,NM_006758.3;U2AF1,missense_variant,p.Asp233Asn,ENST00000380276,NM_001025203.1;U2AF1,3_prime_UTR_variant,,ENST00000464750,;U2AF1,non_coding_transcript_exon_variant,,ENST00000475639,;U2AF1,non_coding_transcript_exon_variant,,ENST00000478282,;U2AF1,non_coding_transcript_exon_variant,,ENST00000471250,;U2AF1,downstream_gene_variant,,ENST00000463599,;U2AF1,downstream_gene_variant,,ENST00000486519,;U2AF1,downstream_gene_variant,,ENST00000496462,; T ENSG00000160201 ENST00000291552 Transcript missense_variant 773/945 697/723 233/240 D/N Gat/Aat 1 -1 U2AF1 HGNC HGNC:12453 protein_coding YES CCDS13694.1 ENSP00000291552 Q01081.241 UPI0000000C26 NM_006758.3 tolerated_low_confidence(0.09) unknown(0) 8/8 Low_complexity_(Seg):seg,PANTHER:PTHR12620,MobiDB_lite:mobidb-lite,MobiDB_lite:mobidb-lite,AlphaFold_DB_import:AF-Q01081-F1 MODERATE 1 SNV 1 1 . TCT . . 43093128 +U2AF1 7307 . GRCh38 21 43104375 43104375 + Silent SNP A A G rs755067307 TUMOR NORMAL A A c.72T>C p.Ile24= p.I24= ENST00000291552 2/8 667 607 60 0 . . U2AF1,synonymous_variant,p.Ile24=,ENST00000291552,NM_006758.3;U2AF1,synonymous_variant,p.Ile24=,ENST00000380276,NM_001025203.1;U2AF1,5_prime_UTR_variant,,ENST00000459639,NM_001025204.2;,upstream_gene_variant,,ENST00000668861,;U2AF1,synonymous_variant,p.Ile24=,ENST00000464750,;U2AF1,synonymous_variant,p.Ile24=,ENST00000486519,;U2AF1,non_coding_transcript_exon_variant,,ENST00000475639,;U2AF1,non_coding_transcript_exon_variant,,ENST00000496462,;U2AF1,non_coding_transcript_exon_variant,,ENST00000463599,;U2AF1,upstream_gene_variant,,ENST00000468039,;,regulatory_region_variant,,ENSR00001365846,; G ENSG00000160201 ENST00000291552 Transcript synonymous_variant 148/945 72/723 24/240 I atT/atC rs755067307 1 -1 U2AF1 HGNC HGNC:12453 protein_coding YES CCDS13694.1 ENSP00000291552 Q01081.241 UPI0000000C26 NM_006758.3 2/8 PROSITE_profiles:PS50103,PANTHER:PTHR12620,Pfam:PF00642,SMART:SM00356,Prints:PR01848,AlphaFold_DB_import:AF-Q01081-F1 LOW 1 SNV 1 1 . CAA . . 7.992e-06 2.921e-05 8.823e-06 43104375 +SIK1 150094 . GRCh38 21 43419117 43419117 + Missense_Mutation SNP C C T novel TUMOR NORMAL C C c.1366G>A p.Glu456Lys p.E456K ENST00000270162 11/14 113 . 45 0 . . SIK1,missense_variant,p.Glu456Lys,ENST00000270162,NM_173354.5;SIK1,downstream_gene_variant,,ENST00000644750,;SIK1,downstream_gene_variant,,ENST00000478426,;SIK1,downstream_gene_variant,,ENST00000644689,;SIK1,downstream_gene_variant,,ENST00000644871,; T ENSG00000142178 ENST00000270162 Transcript missense_variant 1502/4747 1366/2352 456/783 E/K Gag/Aag 1 -1 SIK1 HGNC HGNC:11142 protein_coding YES CCDS33575.1 ENSP00000270162 P57059.208 UPI0000206F2B NM_173354.5 deleterious(0.03) possibly_damaging(0.505) 11/14 PIRSF:PIRSF037014,MobiDB_lite:mobidb-lite,AlphaFold_DB_import:AF-P57059-F1 MODERATE 1 SNV 1 1 . TCC . . 43419117 +ICOSLG 23308 . GRCh38 21 44235374 44235374 + Missense_Mutation SNP C C A TUMOR NORMAL C C c.595G>T p.Val199Leu p.V199L ENST00000407780 4/7 101 88 13 153 153 0 ICOSLG,missense_variant,p.Val199Leu,ENST00000407780,NM_015259.6;ICOSLG,missense_variant,p.Val199Leu,ENST00000400379,;ICOSLG,missense_variant,p.Val199Leu,ENST00000643466,;ICOSLG,missense_variant,p.Val199Leu,ENST00000700361,;ICOSLG,missense_variant,p.Val82Leu,ENST00000400377,NM_001283051.2;ICOSLG,missense_variant,p.Val158Leu,ENST00000700352,;ICOSLG,missense_variant,p.Val199Leu,ENST00000700355,NM_001395918.1;ICOSLG,missense_variant,p.Val114Leu,ENST00000700358,NM_001283052.2,NM_001365759.2;ICOSLG,missense_variant,p.Val199Leu,ENST00000344330,NM_001283050.2;ICOSLG,missense_variant,p.Val114Leu,ENST00000700360,;ICOSLG,3_prime_UTR_variant,,ENST00000700350,;ICOSLG,3_prime_UTR_variant,,ENST00000700356,;ICOSLG,3_prime_UTR_variant,,ENST00000700357,;ICOSLG,3_prime_UTR_variant,,ENST00000700359,;ICOSLG,non_coding_transcript_exon_variant,,ENST00000700354,;ICOSLG,non_coding_transcript_exon_variant,,ENST00000700351,;ICOSLG,non_coding_transcript_exon_variant,,ENST00000700353,; A ENSG00000160223 ENST00000407780 Transcript missense_variant 721/7078 595/909 199/302 V/L Gtg/Ttg COSV60266097 1 -1 ICOSLG HGNC HGNC:17087 protein_coding YES CCDS42952.1 ENSP00000384432 O75144.200 A0N0L8.135 UPI0000049DCB NM_015259.6 deleterious(0) possibly_damaging(0.807) 4/7 Gene3D:2.60.40.10,PDB-ENSP_mappings:6x4g.C,PDB-ENSP_mappings:6x4t.A,PDB-ENSP_mappings:6x4t.C,AlphaFold_DB_import:AF-O75144-F1,PROSITE_profiles:PS50835,PANTHER:PTHR24100,Superfamily:SSF48726 1 MODERATE 1 SNV 1 1 . ACG . . 44235374 +ICOSLG 23308 . GRCh38 21 44236903 44236903 + Missense_Mutation SNP C C T novel TUMOR NORMAL C C c.370G>A p.Glu124Lys p.E124K ENST00000407780 3/7 950 827 123 630 629 1 ICOSLG,missense_variant,p.Glu124Lys,ENST00000407780,NM_015259.6;ICOSLG,missense_variant,p.Glu124Lys,ENST00000400379,;ICOSLG,missense_variant,p.Glu124Lys,ENST00000643466,;ICOSLG,missense_variant,p.Glu124Lys,ENST00000700361,;ICOSLG,missense_variant,p.Glu83Lys,ENST00000700352,;ICOSLG,missense_variant,p.Glu124Lys,ENST00000700355,NM_001395918.1;ICOSLG,missense_variant,p.Glu39Lys,ENST00000700358,NM_001283052.2,NM_001365759.2;ICOSLG,missense_variant,p.Glu124Lys,ENST00000344330,NM_001283050.2;ICOSLG,missense_variant,p.Glu39Lys,ENST00000700360,;ICOSLG,intron_variant,,ENST00000400377,NM_001283051.2;,upstream_gene_variant,,ENST00000619053,;ICOSLG,missense_variant,p.Gly73Glu,ENST00000700359,;ICOSLG,3_prime_UTR_variant,,ENST00000700350,;ICOSLG,3_prime_UTR_variant,,ENST00000700356,;ICOSLG,3_prime_UTR_variant,,ENST00000700357,;ICOSLG,non_coding_transcript_exon_variant,,ENST00000700354,;ICOSLG,non_coding_transcript_exon_variant,,ENST00000700351,;ICOSLG,non_coding_transcript_exon_variant,,ENST00000700353,; T ENSG00000160223 ENST00000407780 Transcript missense_variant 496/7078 370/909 124/302 E/K Gag/Aag 1 -1 ICOSLG HGNC HGNC:17087 protein_coding YES CCDS42952.1 ENSP00000384432 O75144.200 A0N0L8.135 UPI0000049DCB NM_015259.6 tolerated(1) benign(0.003) 3/7 Gene3D:2.60.40.10,PDB-ENSP_mappings:6x4g.C,PDB-ENSP_mappings:6x4t.A,PDB-ENSP_mappings:6x4t.C,AlphaFold_DB_import:AF-O75144-F1,Pfam:PF07686,PROSITE_profiles:PS50835,PANTHER:PTHR24100,SMART:SM00409,Superfamily:SSF48726,CDD:cd20935 MODERATE 1 SNV 1 . TCC . . 44236903 +ICOSLG 23308 . GRCh38 21 44237111 44237111 + Nonsense_Mutation SNP C C T novel TUMOR NORMAL C C c.162G>A p.Trp54Ter p.W54* ENST00000407780 3/7 944 745 199 596 596 0 ICOSLG,stop_gained,p.Trp54Ter,ENST00000407780,NM_015259.6;ICOSLG,stop_gained,p.Trp54Ter,ENST00000400379,;ICOSLG,stop_gained,p.Trp54Ter,ENST00000643466,;ICOSLG,stop_gained,p.Trp54Ter,ENST00000700361,;ICOSLG,stop_gained,p.Trp54Ter,ENST00000700355,NM_001395918.1;ICOSLG,stop_gained,p.Trp54Ter,ENST00000344330,NM_001283050.2;ICOSLG,5_prime_UTR_variant,,ENST00000700358,NM_001283052.2,NM_001365759.2;ICOSLG,intron_variant,,ENST00000400377,NM_001283051.2;ICOSLG,intron_variant,,ENST00000700352,;ICOSLG,intron_variant,,ENST00000700360,;,upstream_gene_variant,,ENST00000619053,;ICOSLG,3_prime_UTR_variant,,ENST00000700350,;ICOSLG,3_prime_UTR_variant,,ENST00000700356,;ICOSLG,3_prime_UTR_variant,,ENST00000700357,;ICOSLG,non_coding_transcript_exon_variant,,ENST00000700354,;ICOSLG,non_coding_transcript_exon_variant,,ENST00000700351,;ICOSLG,intron_variant,,ENST00000700359,;ICOSLG,upstream_gene_variant,,ENST00000700353,;,regulatory_region_variant,,ENSR00001237806,; T ENSG00000160223 ENST00000407780 Transcript stop_gained 288/7078 162/909 54/302 W/* tgG/tgA 1 -1 ICOSLG HGNC HGNC:17087 protein_coding YES CCDS42952.1 ENSP00000384432 O75144.200 A0N0L8.135 UPI0000049DCB NM_015259.6 3/7 Gene3D:2.60.40.10,PDB-ENSP_mappings:6x4g.C,PDB-ENSP_mappings:6x4t.A,PDB-ENSP_mappings:6x4t.C,AlphaFold_DB_import:AF-O75144-F1,Pfam:PF07686,PROSITE_profiles:PS50835,PANTHER:PTHR24100,SMART:SM00409,Superfamily:SSF48726,CDD:cd20935 HIGH 1 SNV 1 . GCC . . 44237111 diff --git a/tests/test_b38_output.more.maf b/tests/test_b38_output.more.maf index d000769..c3cd6d3 100644 --- a/tests/test_b38_output.more.maf +++ b/tests/test_b38_output.more.maf @@ -1,27 +1,27 @@ #version 2.4 -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND_VEP SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS AF AFR_AF AMR_AF ASN_AF EAS_AF EUR_AF SAS_AF AA_AF EA_AF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO MINIMISED GENE_PHENO FILTER flanking_bps vcf_id vcf_qual gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF gnomAD_AC vcf_pos t_GT n_GT -RUNX1 861 mskcc.org GRCh38 21 34792292 34792292 + Missense_Mutation SNP A A C novel MSK_T001 MSK_N001 A A c.1286T>G p.Leu429Arg p.L429R ENST00000300305 8/8 54 . 21 0 . . RUNX1,missense_variant,p.Leu402Arg,ENST00000344691,NM_001001890.3;RUNX1,missense_variant,p.Leu429Arg,ENST00000300305,;RUNX1,missense_variant,p.Leu429Arg,ENST00000675419,NM_001754.5;RUNX1,missense_variant,p.Leu429Arg,ENST00000437180,;RUNX1,missense_variant,p.Leu338Arg,ENST00000399240,;RUNX1,3_prime_UTR_variant,,ENST00000482318,; C ENSG00000159216 ENST00000300305 Transcript missense_variant 1731/6222 1286/1443 429/480 L/R cTg/cGg 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196.238 UPI000015FE6A deleterious(0) possibly_damaging(0.887) 8/8 PANTHER:PTHR11950:SF40,PANTHER:PTHR11950,PIRSF:PIRSF009374,Pfam:PF08504,Prints:PR00967 MODERATE 1 SNV 1 1 . CAG . . 34792292 0/1 0/0 -RUNX1 861 mskcc.org GRCh38 21 34792478 34792478 + Missense_Mutation SNP C C T rs867474432 MSK_T001 MSK_N001 C C c.1100G>A p.Gly367Asp p.G367D ENST00000300305 8/8 901 778 123 482 482 0 RUNX1,missense_variant,p.Gly340Asp,ENST00000344691,NM_001001890.3;RUNX1,missense_variant,p.Gly367Asp,ENST00000300305,;RUNX1,missense_variant,p.Gly367Asp,ENST00000675419,NM_001754.5;RUNX1,missense_variant,p.Gly367Asp,ENST00000437180,;RUNX1,missense_variant,p.Gly276Asp,ENST00000399240,;RUNX1,3_prime_UTR_variant,,ENST00000482318,; T ENSG00000159216 ENST00000300305 Transcript missense_variant 1545/6222 1100/1443 367/480 G/D gGc/gAc rs867474432,COSV55867253 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196.238 UPI000015FE6A deleterious(0.01) possibly_damaging(0.568) 8/8 Low_complexity_(Seg):seg,PANTHER:PTHR11950:SF40,PANTHER:PTHR11950,PIRSF:PIRSF009374,Gene3D:4.10.770.10 0,1 MODERATE 1 SNV 1 0,1 1 . GCC . . 34792478 0/1 0/0 -RUNX1 861 mskcc.org GRCh38 21 34880549 34880549 + Splice_Region SNP T T C novel MSK_T001 MSK_N001 T T c.508+8A>G ENST00000300305 504 450 54 0 . . RUNX1,splice_region_variant,,ENST00000300305,;RUNX1,splice_region_variant,,ENST00000344691,NM_001001890.3;RUNX1,splice_region_variant,,ENST00000358356,NM_001122607.2;RUNX1,splice_region_variant,,ENST00000399237,;RUNX1,splice_region_variant,,ENST00000399240,;RUNX1,splice_region_variant,,ENST00000437180,;RUNX1,splice_region_variant,,ENST00000675419,NM_001754.5;RUNX1,downstream_gene_variant,,ENST00000455571,;AP000331.1,intron_variant,,ENST00000651798,;RUNX1,splice_region_variant,,ENST00000482318,; C ENSG00000159216 ENST00000300305 Transcript splice_region_variant,intron_variant 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196.238 UPI000015FE6A 4/7 LOW 1 SNV 1 1 . ATA . . 34880549 0/1 0/0 -RUNX1 861 mskcc.org GRCh38 21 34880555 34880556 + Splice_Site INS - - CCTCTT novel MSK_T001 MSK_N001 - - c.504_508+1dup p.X168_splice ENST00000300305 883 658 225 343 343 0 RUNX1,splice_donor_variant,,ENST00000300305,;RUNX1,splice_donor_variant,,ENST00000344691,NM_001001890.3;RUNX1,splice_donor_variant,,ENST00000358356,NM_001122607.2;RUNX1,splice_donor_variant,,ENST00000399237,;RUNX1,splice_donor_variant,,ENST00000399240,;RUNX1,splice_donor_variant,,ENST00000437180,;RUNX1,splice_donor_variant,,ENST00000675419,NM_001754.5;RUNX1,downstream_gene_variant,,ENST00000455571,;AP000331.1,intron_variant,,ENST00000651798,;RUNX1,splice_donor_variant,,ENST00000482318,; CCTCTT ENSG00000159216 ENST00000300305 Transcript splice_donor_variant 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196.238 UPI000015FE6A 4/7 HIGH 1 insertion 1 1 . TAC . . 34880555 0/1 0/0 -RUNX1 861 mskcc.org GRCh38 21 34880595 34880595 + Missense_Mutation SNP C C T MSK_T001 MSK_N001 C C c.470G>A p.Arg157Lys p.R157K ENST00000300305 4/8 862 788 74 523 522 1 RUNX1,missense_variant,p.Arg130Lys,ENST00000344691,NM_001001890.3;RUNX1,missense_variant,p.Arg157Lys,ENST00000300305,;RUNX1,missense_variant,p.Arg157Lys,ENST00000675419,NM_001754.5;RUNX1,missense_variant,p.Arg157Lys,ENST00000437180,;RUNX1,missense_variant,p.Arg130Lys,ENST00000358356,NM_001122607.2;RUNX1,missense_variant,p.Arg130Lys,ENST00000399240,;RUNX1,missense_variant,p.Arg145Lys,ENST00000399237,;RUNX1,downstream_gene_variant,,ENST00000455571,;AP000331.1,intron_variant,,ENST00000651798,;RUNX1,3_prime_UTR_variant,,ENST00000482318,; T ENSG00000159216 ENST00000300305 Transcript missense_variant 915/6222 470/1443 157/480 R/K aGa/aAa COSV55871984,COSV55885034 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196.238 UPI000015FE6A tolerated(0.16) probably_damaging(0.978) 4/8 PROSITE_profiles:PS51062,PANTHER:PTHR11950:SF40,PANTHER:PTHR11950,PIRSF:PIRSF009374,Gene3D:2.60.40.720,Pfam:PF00853,Superfamily:SSF49417,Prints:PR00967 1,1 MODERATE 1 SNV 1 1,1 1 . TCT . . 34880595 0/1 0/0 -RUNX1 861 mskcc.org GRCh38 21 34880650 34880651 + Frame_Shift_Ins INS - - G novel MSK_T001 MSK_N001 - - c.414_415insC p.Asn139GlnfsTer5 p.N139Qfs*5 ENST00000300305 4/8 611 449 162 528 527 1 RUNX1,frameshift_variant,p.Asn112GlnfsTer5,ENST00000344691,NM_001001890.3;RUNX1,frameshift_variant,p.Asn139GlnfsTer5,ENST00000300305,;RUNX1,frameshift_variant,p.Asn139GlnfsTer5,ENST00000675419,NM_001754.5;RUNX1,frameshift_variant,p.Asn139GlnfsTer5,ENST00000437180,;RUNX1,frameshift_variant,p.Asn112GlnfsTer5,ENST00000358356,NM_001122607.2;RUNX1,frameshift_variant,p.Asn112GlnfsTer5,ENST00000399240,;RUNX1,frameshift_variant,p.Asn127GlnfsTer5,ENST00000399237,;RUNX1,frameshift_variant,p.Asn126GlnfsTer5,ENST00000455571,;AP000331.1,intron_variant,,ENST00000651798,;RUNX1,3_prime_UTR_variant,,ENST00000482318,; G ENSG00000159216 ENST00000300305 Transcript frameshift_variant 859-860/6222 414-415/1443 138-139/480 -/X -/C 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196.238 UPI000015FE6A 4/8 PROSITE_profiles:PS51062,PANTHER:PTHR11950:SF40,PANTHER:PTHR11950,PIRSF:PIRSF009374,Gene3D:2.60.40.720,Pfam:PF00853,Superfamily:SSF49417,Prints:PR00967 HIGH 1 insertion 1 1 . TTT . . 34880650 0/1 0/0 -RUNX1 861 mskcc.org GRCh38 21 34886911 34886911 + Missense_Mutation SNP G G A novel MSK_T001 MSK_N001 G G c.283C>T p.Pro95Ser p.P95S ENST00000300305 3/8 51 34 17 0 . . RUNX1,missense_variant,p.Pro68Ser,ENST00000344691,NM_001001890.3;RUNX1,missense_variant,p.Pro95Ser,ENST00000300305,;RUNX1,missense_variant,p.Pro95Ser,ENST00000675419,NM_001754.5;RUNX1,missense_variant,p.Pro95Ser,ENST00000437180,;RUNX1,missense_variant,p.Pro68Ser,ENST00000358356,NM_001122607.2;RUNX1,missense_variant,p.Pro68Ser,ENST00000399240,;RUNX1,missense_variant,p.Pro83Ser,ENST00000399237,;RUNX1,missense_variant,p.Pro82Ser,ENST00000455571,;RUNX1,downstream_gene_variant,,ENST00000475045,;AP000331.1,downstream_gene_variant,,ENST00000651798,;RUNX1,intron_variant,,ENST00000482318,;,regulatory_region_variant,,ENSR00000141768,; A ENSG00000159216 ENST00000300305 Transcript missense_variant 728/6222 283/1443 95/480 P/S Ccc/Tcc 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196.238 UPI000015FE6A deleterious(0) probably_damaging(0.997) 3/8 PROSITE_profiles:PS51062,PANTHER:PTHR11950:SF40,PANTHER:PTHR11950,PIRSF:PIRSF009374,Gene3D:2.60.40.720,Pfam:PF00853,Superfamily:SSF49417,Prints:PR00967,Prints:PR00967 MODERATE 1 SNV 1 1 . GGG . . 34886911 0/1 0/0 -SETD4 54093 mskcc.org GRCh38 21 36043782 36043782 + Missense_Mutation SNP C C G novel MSK_T001 MSK_N001 C C c.901G>C p.Glu301Gln p.E301Q ENST00000399215 6/10 1140 1010 130 975 975 0 SETD4,missense_variant,p.Glu301Gln,ENST00000399215,;SETD4,missense_variant,p.Glu277Gln,ENST00000399212,NM_001286752.2;SETD4,missense_variant,p.Glu301Gln,ENST00000332131,NM_017438.5;SETD4,missense_variant,p.Gly277Arg,ENST00000399201,;SETD4,missense_variant,p.Gly277Arg,ENST00000399205,NM_001007261.2;SETD4,missense_variant,p.Gly301Arg,ENST00000399208,NM_001007259.2;SETD4,missense_variant,p.Gly301Arg,ENST00000399207,;SETD4,downstream_gene_variant,,ENST00000424303,;SETD4,downstream_gene_variant,,ENST00000429161,;SETD4,downstream_gene_variant,,ENST00000442559,;SETD4,downstream_gene_variant,,ENST00000446166,;SETD4,splice_region_variant,,ENST00000481477,;SETD4,upstream_gene_variant,,ENST00000469482,;SETD4,downstream_gene_variant,,ENST00000485865,;SETD4,upstream_gene_variant,,ENST00000487297,; G ENSG00000185917 ENST00000399215 Transcript missense_variant,splice_region_variant 2274/4272 901/1323 301/440 E/Q Gaa/Caa 1 -1 SETD4 HGNC HGNC:1258 protein_coding YES CCDS13640.1 ENSP00000382163 Q9NVD3.158 UPI000012868E deleterious(0.01) benign(0.203) 6/10 PANTHER:PTHR13271,PANTHER:PTHR13271:SF8,PIRSF:PIRSF027158 MODERATE 1 SNV 2 . CCT . . 36043782 0/1 0/0 -ERG 2078 mskcc.org GRCh38 21 38383625 38383625 + Silent SNP T T C novel MSK_T001 MSK_N001 T T c.1239A>G p.Ser413= p.S413= ENST00000417133 12/12 352 329 23 0 . . ERG,synonymous_variant,p.Ser389=,ENST00000442448,NM_004449.4;ERG,synonymous_variant,p.Ser413=,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,synonymous_variant,p.Ser390=,ENST00000398910,NM_001291391.1;ERG,synonymous_variant,p.Ser389=,ENST00000398911,;ERG,synonymous_variant,p.Ser406=,ENST00000288319,NM_182918.4;ERG,synonymous_variant,p.Ser383=,ENST00000398907,;ERG,synonymous_variant,p.Ser382=,ENST00000398905,NM_001331025.2;ERG,synonymous_variant,p.Ser290=,ENST00000398897,NM_001243429.1;ERG,synonymous_variant,p.Ser413=,ENST00000398919,NM_001243428.1;ERG,synonymous_variant,p.Ser314=,ENST00000453032,NM_001136155.1; C ENSG00000157554 ENST00000417133 Transcript synonymous_variant 1425/5023 1239/1461 413/486 S tcA/tcG 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS46648.1 ENSP00000414150 P11308.209 UPI000018681C NM_001243432.2,NM_001136154.1 12/12 PANTHER:PTHR11849,PANTHER:PTHR11849:SF216,Superfamily:SSF46785 LOW 1 SNV 2 1 . ATG . . 38383625 0/1 0/0 -ERG 2078 mskcc.org GRCh38 21 38400597 38400597 + Missense_Mutation SNP G G A MSK_T001 MSK_N001 G G c.743C>T p.Thr248Met p.T248M ENST00000417133 8/12 1199 892 307 567 566 1 ERG,missense_variant,p.Thr248Met,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,missense_variant,p.Thr248Met,ENST00000398910,NM_001291391.1;ERG,missense_variant,p.Thr241Met,ENST00000288319,NM_182918.4;ERG,missense_variant,p.Thr241Met,ENST00000398907,;ERG,missense_variant,p.Thr248Met,ENST00000398919,NM_001243428.1;ERG,missense_variant,p.Thr149Met,ENST00000453032,NM_001136155.1;ERG,missense_variant,p.Thr209Met,ENST00000429727,;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398905,NM_001331025.2;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,non_coding_transcript_exon_variant,,ENST00000492833,;ERG,intron_variant,,ENST00000481609,;ERG,downstream_gene_variant,,ENST00000473107,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,;,regulatory_region_variant,,ENSR00000662899,; A ENSG00000157554 ENST00000417133 Transcript missense_variant 929/5023 743/1461 248/486 T/M aCg/aTg COSV55741264 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS46648.1 ENSP00000414150 P11308.209 UPI000018681C NM_001243432.2,NM_001136154.1 tolerated(0.19) benign(0.39) 8/12 PANTHER:PTHR11849,PANTHER:PTHR11849:SF216 1 MODERATE 1 SNV 2 1 1 . CGT . . 38400597 0/1 0/0 -ERG 2078 mskcc.org GRCh38 21 38400606 38400606 + Missense_Mutation SNP G G T MSK_T001 MSK_N001 G G c.734C>A p.Pro245His p.P245H ENST00000417133 8/12 343 190 153 507 507 0 ERG,missense_variant,p.Pro245His,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,missense_variant,p.Pro245His,ENST00000398910,NM_001291391.1;ERG,missense_variant,p.Pro238His,ENST00000288319,NM_182918.4;ERG,missense_variant,p.Pro238His,ENST00000398907,;ERG,missense_variant,p.Pro245His,ENST00000398919,NM_001243428.1;ERG,missense_variant,p.Pro146His,ENST00000453032,NM_001136155.1;ERG,missense_variant,p.Pro206His,ENST00000429727,;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398905,NM_001331025.2;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,non_coding_transcript_exon_variant,,ENST00000492833,;ERG,intron_variant,,ENST00000481609,;ERG,downstream_gene_variant,,ENST00000473107,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,;,regulatory_region_variant,,ENSR00000662899,; T ENSG00000157554 ENST00000417133 Transcript missense_variant 920/5023 734/1461 245/486 P/H cCt/cAt COSV55741651 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS46648.1 ENSP00000414150 P11308.209 UPI000018681C NM_001243432.2,NM_001136154.1 tolerated(0.1) benign(0.227) 8/12 PANTHER:PTHR11849,PANTHER:PTHR11849:SF216 1 MODERATE 1 SNV 2 1 1 . AGG . . 38400606 0/1 0/0 -ERG 2078 mskcc.org GRCh38 21 38403659 38403659 + Missense_Mutation SNP C C T novel MSK_T001 MSK_N001 C C c.460G>A p.Val154Met p.V154M ENST00000417133 6/12 287 149 138 0 . . ERG,missense_variant,p.Val154Met,ENST00000442448,NM_004449.4;ERG,missense_variant,p.Val154Met,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,missense_variant,p.Val154Met,ENST00000398910,NM_001291391.1;ERG,missense_variant,p.Val154Met,ENST00000398911,;ERG,missense_variant,p.Val147Met,ENST00000288319,NM_182918.4;ERG,missense_variant,p.Val147Met,ENST00000398907,;ERG,missense_variant,p.Val147Met,ENST00000398905,NM_001331025.2;ERG,missense_variant,p.Val55Met,ENST00000398897,NM_001243429.1;ERG,missense_variant,p.Val154Met,ENST00000398919,NM_001243428.1;ERG,missense_variant,p.Val55Met,ENST00000453032,NM_001136155.1;ERG,missense_variant,p.Val115Met,ENST00000429727,;ERG,non_coding_transcript_exon_variant,,ENST00000481609,;ERG,non_coding_transcript_exon_variant,,ENST00000492833,;ERG,non_coding_transcript_exon_variant,,ENST00000473107,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,; T ENSG00000157554 ENST00000417133 Transcript missense_variant 646/5023 460/1461 154/486 V/M Gtg/Atg 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS46648.1 ENSP00000414150 P11308.209 UPI000018681C NM_001243432.2,NM_001136154.1 deleterious(0.04) possibly_damaging(0.76) 6/12 Gene3D:1.10.150.50,PDB-ENSP_mappings:1sxe.A,Pfam:PF02198,PROSITE_profiles:PS51433,PANTHER:PTHR11849,PANTHER:PTHR11849:SF216,SMART:SM00251,Superfamily:SSF47769,CDD:cd08540 MODERATE 1 SNV 2 1 . ACC . . 38403659 0/1 0/0 -ERG 2078 mskcc.org GRCh38 21 38575684 38575684 + Missense_Mutation SNP G G A rs201302788 MSK_T001 MSK_N001 G G c.17C>T p.Pro6Leu p.P6L ENST00000417133 3/12 191 92 99 0 . . ERG,missense_variant,p.Pro6Leu,ENST00000442448,NM_004449.4;ERG,missense_variant,p.Pro6Leu,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,missense_variant,p.Pro6Leu,ENST00000398910,NM_001291391.1;ERG,missense_variant,p.Pro6Leu,ENST00000398911,;ERG,missense_variant,p.Pro6Leu,ENST00000398919,NM_001243428.1;ERG,5_prime_UTR_variant,,ENST00000398897,NM_001243429.1;ERG,5_prime_UTR_variant,,ENST00000429727,;ERG,non_coding_transcript_exon_variant,,ENST00000485493,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,; A ENSG00000157554 ENST00000417133 Transcript missense_variant 203/5023 17/1461 6/486 P/L cCg/cTg rs201302788 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS46648.1 ENSP00000414150 P11308.209 UPI000018681C NM_001243432.2,NM_001136154.1 deleterious_low_confidence(0) benign(0.001) 3/12 0.0001163 MODERATE 1 SNV 2 1 . CGG . . 4.776e-05 0.0001056 12 38575684 0/1 0/0 -ERG 2078 mskcc.org GRCh38 21 38575698 38575698 + Translation_Start_Site SNP C C T MSK_T001 MSK_N001 C C c.3G>A p.Met1? p.M1? ENST00000417133 3/12 331 223 96 449 442 0 ERG,start_lost,p.Met1?,ENST00000442448,NM_004449.4;ERG,start_lost,p.Met1?,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,start_lost,p.Met1?,ENST00000398910,NM_001291391.1;ERG,start_lost,p.Met1?,ENST00000398911,;ERG,start_lost,p.Met1?,ENST00000398919,NM_001243428.1;ERG,5_prime_UTR_variant,,ENST00000398897,NM_001243429.1;ERG,5_prime_UTR_variant,,ENST00000429727,;ERG,non_coding_transcript_exon_variant,,ENST00000485493,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,; T ENSG00000157554 ENST00000417133 Transcript start_lost 189/5023 3/1461 1/486 M/I atG/atA COSV67366082 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS46648.1 ENSP00000414150 P11308.209 UPI000018681C NM_001243432.2,NM_001136154.1 deleterious_low_confidence(0.03) benign(0.38) 3/12 1 HIGH 1 SNV 2 1 1 . TCA . . 38575698 0/1 0/0 -TMPRSS2 7113 mskcc.org GRCh38 21 41479183 41479183 + Frame_Shift_Del DEL T T - novel MSK_T001 MSK_N001 T T c.831del p.Lys277AsnfsTer19 p.K277Nfs*19 ENST00000679263 7/14 512 435 77 695 695 0 TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000676973,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000679054,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000678348,;TMPRSS2,frameshift_variant,p.Lys277AsnfsTer19,ENST00000679263,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000332149,NM_005656.4;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000678171,NM_001382720.1;TMPRSS2,frameshift_variant,p.Lys155AsnfsTer19,ENST00000679016,;TMPRSS2,frameshift_variant,p.Lys261AsnfsTer19,ENST00000398585,NM_001135099.1;TMPRSS2,frameshift_variant,p.Lys116AsnfsTer19,ENST00000678743,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000454499,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000458356,;TMPRSS2,frameshift_variant,p.Lys184AsnfsTer19,ENST00000424093,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000678617,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000679181,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer16,ENST00000677680,;TMPRSS2,3_prime_UTR_variant,,ENST00000678959,;,regulatory_region_variant,,ENSR00001056496,; - ENSG00000184012 ENST00000679263 Transcript frameshift_variant 974/3623 831/1638 277/545 K/X aaA/aa 1 -1 TMPRSS2 HGNC HGNC:11876 protein_coding YES ENSP00000504602 7/14 Pfam:PF15494,Gene3D:3.10.250.10,SMART:SM00202,Superfamily:SSF56487,PANTHER:PTHR24253,PANTHER:PTHR24253:SF89 HIGH 1 deletion 1 . AGTT . . 41479182 0/1 0/0 -TMPRSS2 7113 mskcc.org GRCh38 21 41479219 41479219 + Silent SNP C C T novel MSK_T001 MSK_N001 C C c.795G>A p.Leu265= p.L265= ENST00000679263 7/14 1224 782 373 1044 996 0 TMPRSS2,synonymous_variant,p.Leu212=,ENST00000676973,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000679054,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000678348,;TMPRSS2,synonymous_variant,p.Leu265=,ENST00000679263,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000332149,NM_005656.4;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000678171,NM_001382720.1;TMPRSS2,synonymous_variant,p.Leu143=,ENST00000679016,;TMPRSS2,synonymous_variant,p.Leu249=,ENST00000398585,NM_001135099.1;TMPRSS2,synonymous_variant,p.Leu104=,ENST00000678743,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000454499,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000458356,;TMPRSS2,synonymous_variant,p.Leu172=,ENST00000424093,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000678617,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000679181,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000677680,;TMPRSS2,3_prime_UTR_variant,,ENST00000678959,;,regulatory_region_variant,,ENSR00001056496,; T ENSG00000184012 ENST00000679263 Transcript synonymous_variant 938/3623 795/1638 265/545 L ctG/ctA 1 -1 TMPRSS2 HGNC HGNC:11876 protein_coding YES ENSP00000504602 7/14 Pfam:PF15494,Gene3D:3.10.250.10,SMART:SM00202,Superfamily:SSF56487,PANTHER:PTHR24253,PANTHER:PTHR24253:SF89 LOW 1 SNV 1 . TCA . . 41479219 0/1 0/0 -TMPRSS2 7113 mskcc.org GRCh38 21 41488494 41488494 + Missense_Mutation SNP G G T MSK_T001 MSK_N001 G G c.504C>A p.Asn168Lys p.N168K ENST00000679263 5/14 380 350 30 0 . . TMPRSS2,missense_variant,p.Asn115Lys,ENST00000676973,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000679054,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000678348,;TMPRSS2,missense_variant,p.Asn168Lys,ENST00000679263,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000332149,NM_005656.4;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000678171,NM_001382720.1;TMPRSS2,missense_variant,p.Asn152Lys,ENST00000398585,NM_001135099.1;TMPRSS2,missense_variant,p.Asn7Lys,ENST00000678743,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000454499,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,;TMPRSS2,intron_variant,,ENST00000679016,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000678617,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000463138,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000679181,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000677680,;TMPRSS2,3_prime_UTR_variant,,ENST00000678959,; T ENSG00000184012 ENST00000679263 Transcript missense_variant 647/3623 504/1638 168/545 N/K aaC/aaA COSV59825472 1 -1 TMPRSS2 HGNC HGNC:11876 protein_coding YES ENSP00000504602 tolerated(0.95) benign(0.07) 5/14 CDD:cd00112,Gene3D:4.10.400.10,SMART:SM00192,Superfamily:SSF57424,PROSITE_profiles:PS50068,PANTHER:PTHR24253,PANTHER:PTHR24253:SF89 1 MODERATE 1 SNV 1 1 . AGT . . 41488494 0/1 0/0 -TMPRSS2 7113 mskcc.org GRCh38 21 41494550 41494550 + Missense_Mutation SNP T T C rs774327563 MSK_T001 MSK_N001 T T c.203A>G p.Tyr68Cys p.Y68C ENST00000679263 3/14 356 260 96 781 781 0 TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000676973,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000679054,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000678348,;TMPRSS2,missense_variant,p.Tyr68Cys,ENST00000679263,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000332149,NM_005656.4;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000678171,NM_001382720.1;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000679016,;TMPRSS2,missense_variant,p.Tyr52Cys,ENST00000398585,NM_001135099.1;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000454499,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000458356,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000424093,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000455813,;TMPRSS2,intron_variant,,ENST00000678743,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000678617,;TMPRSS2,intron_variant,,ENST00000463138,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000679181,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000677680,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000678959,; C ENSG00000184012 ENST00000679263 Transcript missense_variant 346/3623 203/1638 68/545 Y/C tAt/tGt rs774327563 1 -1 TMPRSS2 HGNC HGNC:11876 protein_coding YES ENSP00000504602 tolerated(0.06) benign(0.412) 3/14 MODERATE 1 SNV 1 . ATA . . 1.995e-05 0.0001232 5.444e-05 1.762e-05 5 41494550 0/1 0/0 -UMODL1 89766 mskcc.org GRCh38 21 42085325 42085325 + Silent SNP C C T rs185422923 MSK_T001 MSK_N001 C C c.516C>T p.Asn172= p.N172= ENST00000408989 4/22 366 193 173 0 . . UMODL1,synonymous_variant,p.Asn100=,ENST00000400424,NM_001199528.3;UMODL1,synonymous_variant,p.Asn100=,ENST00000400427,NM_001199527.2;UMODL1,synonymous_variant,p.Asn172=,ENST00000408989,NM_173568.3;UMODL1,synonymous_variant,p.Asn172=,ENST00000408910,NM_001004416.2;UMODL1,synonymous_variant,p.Asn8=,ENST00000491559,;UMODL1,synonymous_variant,p.Asn8=,ENST00000466434,;UMODL1,synonymous_variant,p.Asn8=,ENST00000400421,;UMODL1,synonymous_variant,p.Asn8=,ENST00000468982,;UMODL1,synonymous_variant,p.Asn8=,ENST00000485357,;UMODL1,synonymous_variant,p.Asn8=,ENST00000497243,; T ENSG00000177398 ENST00000408989 Transcript synonymous_variant 516/5262 516/4341 172/1446 N aaC/aaT rs185422923 1 1 UMODL1 HGNC HGNC:12560 protein_coding YES CCDS42935.1 ENSP00000386126 Q5DID0.131 UPI0000D6254B NM_173568.3 4/22 PANTHER:PTHR14002,PANTHER:PTHR14002:SF22 0.0002 0.0008 0.0001207 LOW 1 SNV 1 . ACG . . 8.016e-06 6.457e-05 3.268e-05 2 42085325 0/1 0/0 -U2AF1 7307 mskcc.org GRCh38 21 43093128 43093128 + Missense_Mutation SNP C C T novel MSK_T001 MSK_N001 C C c.697G>A p.Asp233Asn p.D233N ENST00000291552 8/8 454 425 29 344 344 0 U2AF1,missense_variant,p.Asp160Asn,ENST00000459639,NM_001025204.1;U2AF1,missense_variant,p.Asp233Asn,ENST00000291552,NM_006758.3;U2AF1,missense_variant,p.Asp233Asn,ENST00000380276,NM_001025203.1;U2AF1,3_prime_UTR_variant,,ENST00000464750,;U2AF1,non_coding_transcript_exon_variant,,ENST00000475639,;U2AF1,non_coding_transcript_exon_variant,,ENST00000478282,;U2AF1,non_coding_transcript_exon_variant,,ENST00000471250,;U2AF1,downstream_gene_variant,,ENST00000463599,;U2AF1,downstream_gene_variant,,ENST00000486519,;U2AF1,downstream_gene_variant,,ENST00000496462,; T ENSG00000160201 ENST00000291552 Transcript missense_variant 773/945 697/723 233/240 D/N Gat/Aat 1 -1 U2AF1 HGNC HGNC:12453 protein_coding YES CCDS13694.1 ENSP00000291552 Q01081.224 UPI0000000C26 NM_006758.3 tolerated(0.44) possibly_damaging(0.857) 8/8 PANTHER:PTHR12620,PANTHER:PTHR12620:SF11,MobiDB_lite:mobidb-lite,MobiDB_lite:mobidb-lite,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 . TCT . . 43093128 0/1 0/0 -U2AF1 7307 mskcc.org GRCh38 21 43104375 43104375 + Silent SNP A A G rs755067307 MSK_T001 MSK_N001 A A c.72T>C p.Ile24= p.I24= ENST00000291552 2/8 667 607 60 0 . . U2AF1,synonymous_variant,p.Ile24=,ENST00000291552,NM_006758.3;U2AF1,synonymous_variant,p.Ile24=,ENST00000380276,NM_001025203.1;U2AF1,5_prime_UTR_variant,,ENST00000459639,NM_001025204.1;AP001631.2,upstream_gene_variant,,ENST00000668861,;U2AF1,synonymous_variant,p.Ile24=,ENST00000464750,;U2AF1,synonymous_variant,p.Ile24=,ENST00000486519,;U2AF1,non_coding_transcript_exon_variant,,ENST00000475639,;U2AF1,non_coding_transcript_exon_variant,,ENST00000496462,;U2AF1,non_coding_transcript_exon_variant,,ENST00000463599,;U2AF1,upstream_gene_variant,,ENST00000468039,; G ENSG00000160201 ENST00000291552 Transcript synonymous_variant 148/945 72/723 24/240 I atT/atC rs755067307 1 -1 U2AF1 HGNC HGNC:12453 protein_coding YES CCDS13694.1 ENSP00000291552 Q01081.224 UPI0000000C26 NM_006758.3 2/8 Pfam:PF00642,Prints:PR01848,PROSITE_profiles:PS50103,PANTHER:PTHR12620,PANTHER:PTHR12620:SF11,SMART:SM00356 LOW 1 SNV 1 1 . CAA . . 7.992e-06 2.921e-05 8.823e-06 2 43104375 0/1 0/0 -SIK1 150094 mskcc.org GRCh38 21 43419117 43419117 + Missense_Mutation SNP C C T novel MSK_T001 MSK_N001 C C c.1366G>A p.Glu456Lys p.E456K ENST00000270162 11/14 113 . 45 0 . . SIK1,missense_variant,p.Glu456Lys,ENST00000270162,NM_173354.5;SIK1,downstream_gene_variant,,ENST00000644750,;SIK1,downstream_gene_variant,,ENST00000478426,;SIK1,downstream_gene_variant,,ENST00000644689,;SIK1,downstream_gene_variant,,ENST00000644871,; T ENSG00000142178 ENST00000270162 Transcript missense_variant 1502/4747 1366/2352 456/783 E/K Gag/Aag 1 -1 SIK1 HGNC HGNC:11142 protein_coding YES CCDS33575.1 ENSP00000270162 P57059.191 UPI0000206F2B NM_173354.5 deleterious(0.03) possibly_damaging(0.494) 11/14 PIRSF:PIRSF037014,PANTHER:PTHR24346,PANTHER:PTHR24346:SF47,MobiDB_lite:mobidb-lite MODERATE 1 SNV 1 1 . TCC . . 43419117 0/1 0/0 -ICOSLG 23308 mskcc.org GRCh38 21 44235374 44235374 + Missense_Mutation SNP C C A MSK_T001 MSK_N001 C C c.595G>T p.Val199Leu p.V199L ENST00000400379 4/6 101 88 13 153 153 0 ICOSLG,missense_variant,p.Val199Leu,ENST00000407780,NM_001283052.2,NM_015259.6,NM_001365759.2;ICOSLG,missense_variant,p.Val199Leu,ENST00000400379,;ICOSLG,missense_variant,p.Val82Leu,ENST00000400377,NM_001283051.2;ICOSLG,missense_variant,p.Val199Leu,ENST00000344330,NM_001283050.2; A ENSG00000160223 ENST00000400379 Transcript missense_variant 723/4246 595/1422 199/473 V/L Gtg/Ttg COSV60266097 1 -1 ICOSLG HGNC HGNC:17087 protein_coding YES ENSP00000383230 K4DIA0.68 UPI00003E5A05 tolerated(0.06) probably_damaging(0.982) 4/6 Superfamily:SSF48726,Gene3D:2.60.40.10,PANTHER:PTHR24100,PANTHER:PTHR24100:SF55,PROSITE_profiles:PS50835 1 MODERATE 1 SNV 1 1 . ACG . . 44235374 0/1 0/0 -ICOSLG 23308 mskcc.org GRCh38 21 44236903 44236903 + Missense_Mutation SNP C C T novel MSK_T001 MSK_N001 C C c.370G>A p.Glu124Lys p.E124K ENST00000400379 3/6 950 827 123 630 629 1 ICOSLG,missense_variant,p.Glu124Lys,ENST00000407780,NM_001283052.2,NM_015259.6,NM_001365759.2;ICOSLG,missense_variant,p.Glu124Lys,ENST00000400379,;ICOSLG,missense_variant,p.Glu124Lys,ENST00000344330,NM_001283050.2;ICOSLG,intron_variant,,ENST00000400377,NM_001283051.2;AP001059.2,upstream_gene_variant,,ENST00000619053,; T ENSG00000160223 ENST00000400379 Transcript missense_variant 498/4246 370/1422 124/473 E/K Gag/Aag 1 -1 ICOSLG HGNC HGNC:17087 protein_coding YES ENSP00000383230 K4DIA0.68 UPI00003E5A05 tolerated(0.37) benign(0.031) 3/6 Superfamily:SSF48726,SMART:SM00409,Pfam:PF07686,Gene3D:2.60.40.10,PANTHER:PTHR24100,PANTHER:PTHR24100:SF55,PROSITE_profiles:PS50835 MODERATE 1 SNV 1 . TCC . . 44236903 0/1 0/0 -ICOSLG 23308 mskcc.org GRCh38 21 44237111 44237111 + Nonsense_Mutation SNP C C T novel MSK_T001 MSK_N001 C C c.162G>A p.Trp54Ter p.W54* ENST00000400379 3/6 944 745 199 596 596 0 ICOSLG,stop_gained,p.Trp54Ter,ENST00000407780,NM_001283052.2,NM_015259.6,NM_001365759.2;ICOSLG,stop_gained,p.Trp54Ter,ENST00000400379,;ICOSLG,stop_gained,p.Trp54Ter,ENST00000344330,NM_001283050.2;ICOSLG,intron_variant,,ENST00000400377,NM_001283051.2;AP001059.2,upstream_gene_variant,,ENST00000619053,; T ENSG00000160223 ENST00000400379 Transcript stop_gained 290/4246 162/1422 54/473 W/* tgG/tgA 1 -1 ICOSLG HGNC HGNC:17087 protein_coding YES ENSP00000383230 K4DIA0.68 UPI00003E5A05 3/6 Superfamily:SSF48726,SMART:SM00409,Pfam:PF07686,Gene3D:2.60.40.10,PANTHER:PTHR24100,PANTHER:PTHR24100:SF55,PROSITE_profiles:PS50835 HIGH 1 SNV 1 . GCC . . 44237111 0/1 0/0 +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND_VEP SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS AF AFR_AF AMR_AF ASN_AF EAS_AF EUR_AF SAS_AF AA_AF EA_AF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO MINIMISED GENE_PHENO FILTER flanking_bps vcf_id vcf_qual gnomADe_AF gnomADe_AFR_AF gnomADe_AMR_AF gnomADe_ASJ_AF gnomADe_EAS_AF gnomADe_FIN_AF gnomADe_NFE_AF gnomADe_OTH_AF gnomADe_SAS_AF gnomAD_AC vcf_pos t_GT n_GT +RUNX1 861 mskcc.org GRCh38 21 34792292 34792292 + Missense_Mutation SNP A A C rs2056450952 MSK_T001 MSK_N001 A A c.1286T>G p.Leu429Arg p.L429R ENST00000675419 9/9 54 . 21 0 . . RUNX1,missense_variant,p.Leu402Arg,ENST00000344691,NM_001001890.3;RUNX1,missense_variant,p.Leu429Arg,ENST00000300305,;RUNX1,missense_variant,p.Leu429Arg,ENST00000675419,NM_001754.5;RUNX1,missense_variant,p.Leu338Arg,ENST00000399240,;RUNX1,3_prime_UTR_variant,,ENST00000482318,; C ENSG00000159216 ENST00000675419 Transcript missense_variant 1480/5971 1286/1443 429/480 L/R cTg/cGg rs2056450952 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000501943 Q01196.255 UPI000015FE6A NM_001754.5 deleterious_low_confidence(0) 9/9 AlphaFold_DB_import:AF-Q01196-F1,Pfam:PF08504,PIRSF:PIRSF009374,Prints:PR00967,PANTHER:PTHR11950 uncertain_significance MODERATE 1 SNV 1 1 . CAG . . 34792292 0/1 0/0 +RUNX1 861 mskcc.org GRCh38 21 34792478 34792478 + Missense_Mutation SNP C C T rs867474432 MSK_T001 MSK_N001 C C c.1100G>A p.Gly367Asp p.G367D ENST00000675419 9/9 901 778 123 482 482 0 RUNX1,missense_variant,p.Gly340Asp,ENST00000344691,NM_001001890.3;RUNX1,missense_variant,p.Gly367Asp,ENST00000300305,;RUNX1,missense_variant,p.Gly367Asp,ENST00000675419,NM_001754.5;RUNX1,missense_variant,p.Gly276Asp,ENST00000399240,;RUNX1,3_prime_UTR_variant,,ENST00000482318,; T ENSG00000159216 ENST00000675419 Transcript missense_variant 1294/5971 1100/1443 367/480 G/D gGc/gAc rs867474432,COSV55867253 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000501943 Q01196.255 UPI000015FE6A NM_001754.5 deleterious_low_confidence(0.01) 9/9 Gene3D:4.10.770.10,AlphaFold_DB_import:AF-Q01196-F1,PIRSF:PIRSF009374,PANTHER:PTHR11950,Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 0,1 1 . GCC . . 34792478 0/1 0/0 +RUNX1 861 mskcc.org GRCh38 21 34880549 34880549 + Splice_Region SNP T T C novel MSK_T001 MSK_N001 T T c.508+8A>G ENST00000675419 504 450 54 0 . . RUNX1,splice_region_variant,,ENST00000300305,;RUNX1,splice_region_variant,,ENST00000344691,NM_001001890.3;RUNX1,splice_region_variant,,ENST00000358356,NM_001122607.2;RUNX1,splice_region_variant,,ENST00000399237,;RUNX1,splice_region_variant,,ENST00000399240,;RUNX1,splice_region_variant,,ENST00000675419,NM_001754.5;RUNX1,downstream_gene_variant,,ENST00000455571,;RUNX1-AS1,intron_variant,,ENST00000651798,;RUNX1,splice_region_variant,,ENST00000482318,;,regulatory_region_variant,,ENSR00001365449,; C ENSG00000159216 ENST00000675419 Transcript splice_region_variant,intron_variant 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000501943 Q01196.255 UPI000015FE6A NM_001754.5 5/8 LOW 1 SNV 1 . ATA . . 34880549 0/1 0/0 +RUNX1 861 mskcc.org GRCh38 21 34880555 34880556 + Splice_Site INS - - CCTCTT novel MSK_T001 MSK_N001 - - c.504_508+1dup p.X168_splice ENST00000675419 883 658 225 343 343 0 RUNX1,splice_donor_variant,,ENST00000300305,;RUNX1,splice_donor_variant,,ENST00000344691,NM_001001890.3;RUNX1,splice_donor_variant,,ENST00000358356,NM_001122607.2;RUNX1,splice_donor_variant,,ENST00000399237,;RUNX1,splice_donor_variant,,ENST00000399240,;RUNX1,splice_donor_variant,,ENST00000675419,NM_001754.5;RUNX1,downstream_gene_variant,,ENST00000455571,;RUNX1-AS1,intron_variant,,ENST00000651798,;RUNX1,splice_donor_variant,,ENST00000482318,;,regulatory_region_variant,,ENSR00001365449,; CCTCTT ENSG00000159216 ENST00000675419 Transcript splice_donor_variant 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000501943 Q01196.255 UPI000015FE6A NM_001754.5 5/8 HIGH 1 insertion 1 . TAC . . 34880555 0/1 0/0 +RUNX1 861 mskcc.org GRCh38 21 34880595 34880595 + Missense_Mutation SNP C C T rs2146361175 MSK_T001 MSK_N001 C C c.470G>A p.Arg157Lys p.R157K ENST00000675419 5/9 862 788 74 523 522 1 RUNX1,missense_variant,p.Arg130Lys,ENST00000344691,NM_001001890.3;RUNX1,missense_variant,p.Arg157Lys,ENST00000300305,;RUNX1,missense_variant,p.Arg157Lys,ENST00000675419,NM_001754.5;RUNX1,missense_variant,p.Arg130Lys,ENST00000358356,NM_001122607.2;RUNX1,missense_variant,p.Arg130Lys,ENST00000399240,;RUNX1,missense_variant,p.Arg145Lys,ENST00000399237,;RUNX1,downstream_gene_variant,,ENST00000455571,;RUNX1-AS1,intron_variant,,ENST00000651798,;RUNX1,3_prime_UTR_variant,,ENST00000482318,;,regulatory_region_variant,,ENSR00001365449,; T ENSG00000159216 ENST00000675419 Transcript missense_variant 664/5971 470/1443 157/480 R/K aGa/aAa rs2146361175,COSV55871984,COSV55885034 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000501943 Q01196.255 UPI000015FE6A NM_001754.5 deleterious_low_confidence(0.01) 5/9 Gene3D:2.60.40.720,AlphaFold_DB_import:AF-Q01196-F1,Pfam:PF00853,PIRSF:PIRSF009374,Prints:PR00967,PROSITE_profiles:PS51062,PANTHER:PTHR11950,Superfamily:SSF49417 0,1,1 MODERATE 1 SNV 0,1,1 1 . TCT . . 34880595 0/1 0/0 +RUNX1 861 mskcc.org GRCh38 21 34880650 34880651 + Frame_Shift_Ins INS - - G novel MSK_T001 MSK_N001 - - c.414_415insC p.Asn139GlnfsTer5 p.N139Qfs*5 ENST00000675419 5/9 611 449 162 528 527 1 RUNX1,frameshift_variant,p.Asn112GlnfsTer5,ENST00000344691,NM_001001890.3;RUNX1,frameshift_variant,p.Asn139GlnfsTer5,ENST00000300305,;RUNX1,frameshift_variant,p.Asn139GlnfsTer5,ENST00000675419,NM_001754.5;RUNX1,frameshift_variant,p.Asn112GlnfsTer5,ENST00000358356,NM_001122607.2;RUNX1,frameshift_variant,p.Asn112GlnfsTer5,ENST00000399240,;RUNX1,frameshift_variant,p.Asn127GlnfsTer5,ENST00000399237,;RUNX1,frameshift_variant,p.Asn126GlnfsTer5,ENST00000455571,;RUNX1-AS1,intron_variant,,ENST00000651798,;RUNX1,3_prime_UTR_variant,,ENST00000482318,;,regulatory_region_variant,,ENSR00001365449,; G ENSG00000159216 ENST00000675419 Transcript frameshift_variant 608-609/5971 414-415/1443 138-139/480 -/X -/C 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000501943 Q01196.255 UPI000015FE6A NM_001754.5 5/9 Gene3D:2.60.40.720,AlphaFold_DB_import:AF-Q01196-F1,Pfam:PF00853,PIRSF:PIRSF009374,Prints:PR00967,PROSITE_profiles:PS51062,PANTHER:PTHR11950,Superfamily:SSF49417 HIGH 1 insertion 1 . TTT . . 34880650 0/1 0/0 +RUNX1 861 mskcc.org GRCh38 21 34886911 34886911 + Missense_Mutation SNP G G A rs2057999086 MSK_T001 MSK_N001 G G c.283C>T p.Pro95Ser p.P95S ENST00000675419 4/9 51 34 17 0 . . RUNX1,missense_variant,p.Pro68Ser,ENST00000344691,NM_001001890.3;RUNX1,missense_variant,p.Pro95Ser,ENST00000300305,;RUNX1,missense_variant,p.Pro95Ser,ENST00000675419,NM_001754.5;RUNX1,missense_variant,p.Pro68Ser,ENST00000358356,NM_001122607.2;RUNX1,missense_variant,p.Pro68Ser,ENST00000399240,;RUNX1,missense_variant,p.Pro83Ser,ENST00000399237,;RUNX1,missense_variant,p.Pro82Ser,ENST00000455571,;RUNX1,downstream_gene_variant,,ENST00000475045,;RUNX1-AS1,downstream_gene_variant,,ENST00000651798,;RUNX1,intron_variant,,ENST00000482318,;,regulatory_region_variant,,ENSR00001365449,; A ENSG00000159216 ENST00000675419 Transcript missense_variant 477/5971 283/1443 95/480 P/S Ccc/Tcc rs2057999086 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000501943 Q01196.255 UPI000015FE6A NM_001754.5 deleterious_low_confidence(0.01) 4/9 Gene3D:2.60.40.720,AlphaFold_DB_import:AF-Q01196-F1,Pfam:PF00853,PIRSF:PIRSF009374,Prints:PR00967,Prints:PR00967,PROSITE_profiles:PS51062,PANTHER:PTHR11950,Superfamily:SSF49417 uncertain_significance MODERATE 1 SNV 1 1 . GGG . . 34886911 0/1 0/0 +SETD4 54093 mskcc.org GRCh38 21 36043782 36043782 + Missense_Mutation SNP C C G novel MSK_T001 MSK_N001 C C c.901G>C p.Glu301Gln p.E301Q ENST00000332131 7/12 1140 1010 130 975 975 0 SETD4,missense_variant,p.Glu301Gln,ENST00000399215,;SETD4,missense_variant,p.Glu277Gln,ENST00000399212,NM_001286752.2;SETD4,missense_variant,p.Glu301Gln,ENST00000332131,NM_017438.5;SETD4,missense_variant,p.Gly277Arg,ENST00000399201,;SETD4,missense_variant,p.Gly277Arg,ENST00000399205,NM_001007261.3;SETD4,missense_variant,p.Gly301Arg,ENST00000399208,NM_001007259.3;SETD4,missense_variant,p.Gly301Arg,ENST00000399207,;SETD4,downstream_gene_variant,,ENST00000424303,;SETD4,downstream_gene_variant,,ENST00000429161,;SETD4,downstream_gene_variant,,ENST00000442559,;SETD4,downstream_gene_variant,,ENST00000446166,;SETD4,splice_region_variant,,ENST00000481477,;SETD4,upstream_gene_variant,,ENST00000469482,;SETD4,downstream_gene_variant,,ENST00000485865,;SETD4,upstream_gene_variant,,ENST00000487297,; G ENSG00000185917 ENST00000332131 Transcript missense_variant,splice_region_variant 1117/2991 901/1323 301/440 E/Q Gaa/Caa 1 -1 SETD4 HGNC HGNC:1258 protein_coding YES CCDS13640.1 ENSP00000329189 Q9NVD3.174 UPI000012868E NM_017438.5 deleterious(0) benign(0.21) 7/12 PANTHER:PTHR13271,PIRSF:PIRSF027158,AlphaFold_DB_import:AF-Q9NVD3-F1 MODERATE 1 SNV 2 . CCT . . 36043782 0/1 0/0 +ERG 2078 mskcc.org GRCh38 21 38383625 38383625 + Silent SNP T T C novel MSK_T001 MSK_N001 T T c.1218A>G p.Ser406= p.S406= ENST00000288319 10/10 352 329 23 0 . . ERG,synonymous_variant,p.Ser389=,ENST00000442448,NM_004449.4;ERG,synonymous_variant,p.Ser413=,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,synonymous_variant,p.Ser390=,ENST00000398910,NM_001291391.1;ERG,synonymous_variant,p.Ser389=,ENST00000398911,;ERG,synonymous_variant,p.Ser406=,ENST00000288319,NM_182918.4;ERG,synonymous_variant,p.Ser383=,ENST00000398907,;ERG,synonymous_variant,p.Ser382=,ENST00000398905,NM_001331025.2;ERG,synonymous_variant,p.Ser290=,ENST00000398897,NM_001243429.1;ERG,synonymous_variant,p.Ser413=,ENST00000398919,NM_001243428.1;ERG,synonymous_variant,p.Ser314=,ENST00000453032,NM_001136155.1; C ENSG00000157554 ENST00000288319 Transcript synonymous_variant 1315/4904 1218/1440 406/479 S tcA/tcG 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS13658.1 ENSP00000288319 P11308.226 UPI0000074389 NM_182918.4 10/10 PDB-ENSP_mappings:6vge.A,PDB-ENSP_mappings:6vgg.A,AlphaFold_DB_import:AF-P11308-F1,Superfamily:SSF46785 LOW 1 SNV 1 1 . ATG . . 38383625 0/1 0/0 +ERG 2078 mskcc.org GRCh38 21 38400597 38400597 + Missense_Mutation SNP G G A rs1988442233 MSK_T001 MSK_N001 G G c.722C>T p.Thr241Met p.T241M ENST00000288319 6/10 1199 892 307 567 566 1 ERG,missense_variant,p.Thr248Met,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,missense_variant,p.Thr248Met,ENST00000398910,NM_001291391.1;ERG,missense_variant,p.Thr241Met,ENST00000288319,NM_182918.4;ERG,missense_variant,p.Thr241Met,ENST00000398907,;ERG,missense_variant,p.Thr248Met,ENST00000398919,NM_001243428.1;ERG,missense_variant,p.Thr149Met,ENST00000453032,NM_001136155.1;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398905,NM_001331025.2;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,non_coding_transcript_exon_variant,,ENST00000492833,;ERG,intron_variant,,ENST00000481609,;ERG,downstream_gene_variant,,ENST00000473107,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,;,regulatory_region_variant,,ENSR00000662899,; A ENSG00000157554 ENST00000288319 Transcript missense_variant 819/4904 722/1440 241/479 T/M aCg/aTg rs1988442233,COSV55741264 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS13658.1 ENSP00000288319 P11308.226 UPI0000074389 NM_182918.4 tolerated(0.11) 6/10 AlphaFold_DB_import:AF-P11308-F1,PANTHER:PTHR11849 0,1 MODERATE 1 SNV 1 0,1 1 . CGT . . 38400597 0/1 0/0 +ERG 2078 mskcc.org GRCh38 21 38400606 38400606 + Missense_Mutation SNP G G T MSK_T001 MSK_N001 G G c.713C>A p.Pro238His p.P238H ENST00000288319 6/10 343 190 153 507 507 0 ERG,missense_variant,p.Pro245His,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,missense_variant,p.Pro245His,ENST00000398910,NM_001291391.1;ERG,missense_variant,p.Pro238His,ENST00000288319,NM_182918.4;ERG,missense_variant,p.Pro238His,ENST00000398907,;ERG,missense_variant,p.Pro245His,ENST00000398919,NM_001243428.1;ERG,missense_variant,p.Pro146His,ENST00000453032,NM_001136155.1;ERG,intron_variant,,ENST00000398897,NM_001243429.1;ERG,intron_variant,,ENST00000398905,NM_001331025.2;ERG,intron_variant,,ENST00000398911,;ERG,intron_variant,,ENST00000442448,NM_004449.4;ERG,non_coding_transcript_exon_variant,,ENST00000492833,;ERG,intron_variant,,ENST00000481609,;ERG,downstream_gene_variant,,ENST00000473107,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,;,regulatory_region_variant,,ENSR00000662899,; T ENSG00000157554 ENST00000288319 Transcript missense_variant 810/4904 713/1440 238/479 P/H cCt/cAt COSV55741651 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS13658.1 ENSP00000288319 P11308.226 UPI0000074389 NM_182918.4 deleterious(0.04) 6/10 AlphaFold_DB_import:AF-P11308-F1,PANTHER:PTHR11849 1 MODERATE 1 SNV 1 1 1 . AGG . . 38400606 0/1 0/0 +ERG 2078 mskcc.org GRCh38 21 38403659 38403659 + Missense_Mutation SNP C C T rs1988621553 MSK_T001 MSK_N001 C C c.439G>A p.Val147Met p.V147M ENST00000288319 4/10 287 149 138 0 . . ERG,missense_variant,p.Val154Met,ENST00000442448,NM_004449.4;ERG,missense_variant,p.Val154Met,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,missense_variant,p.Val154Met,ENST00000398910,NM_001291391.1;ERG,missense_variant,p.Val154Met,ENST00000398911,;ERG,missense_variant,p.Val147Met,ENST00000288319,NM_182918.4;ERG,missense_variant,p.Val147Met,ENST00000398907,;ERG,missense_variant,p.Val147Met,ENST00000398905,NM_001331025.2;ERG,missense_variant,p.Val55Met,ENST00000398897,NM_001243429.1;ERG,missense_variant,p.Val154Met,ENST00000398919,NM_001243428.1;ERG,missense_variant,p.Val55Met,ENST00000453032,NM_001136155.1;ERG,non_coding_transcript_exon_variant,,ENST00000481609,;ERG,non_coding_transcript_exon_variant,,ENST00000492833,;ERG,non_coding_transcript_exon_variant,,ENST00000473107,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,; T ENSG00000157554 ENST00000288319 Transcript missense_variant 536/4904 439/1440 147/479 V/M Gtg/Atg rs1988621553 1 -1 ERG HGNC HGNC:3446 protein_coding YES CCDS13658.1 ENSP00000288319 P11308.226 UPI0000074389 NM_182918.4 deleterious(0.02) 4/10 Gene3D:1.10.150.50,PDB-ENSP_mappings:1sxe.A,AlphaFold_DB_import:AF-P11308-F1,Pfam:PF02198,PROSITE_profiles:PS51433,PANTHER:PTHR11849,SMART:SM00251,Superfamily:SSF47769,CDD:cd08540 MODERATE 1 SNV 1 1 . ACC . . 38403659 0/1 0/0 +ERG 2078 mskcc.org GRCh38 21 38575684 38575684 + Missense_Mutation SNP G G A rs201302788 MSK_T001 MSK_N001 G G c.17C>T p.Pro6Leu p.P6L ENST00000442448 3/11 191 92 99 0 . . ERG,missense_variant,p.Pro6Leu,ENST00000442448,NM_004449.4;ERG,missense_variant,p.Pro6Leu,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,missense_variant,p.Pro6Leu,ENST00000398910,NM_001291391.1;ERG,missense_variant,p.Pro6Leu,ENST00000398911,;ERG,missense_variant,p.Pro6Leu,ENST00000398919,NM_001243428.1;ERG,5_prime_UTR_variant,,ENST00000398897,NM_001243429.1;ERG,non_coding_transcript_exon_variant,,ENST00000485493,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,; A ENSG00000157554 ENST00000442448 Transcript missense_variant 289/5034 17/1389 6/462 P/L cCg/cTg rs201302788 1 -1 ERG HGNC HGNC:3446 protein_coding CCDS13657.1 ENSP00000394694 P11308.226 UPI0000046820 NM_004449.4 deleterious_low_confidence(0.01) benign(0.005) 3/11 AlphaFold_DB_import:AF-P11308-F1 MODERATE SNV 5 1 . CGG . . 4.776e-05 0.0001056 12 38575684 0/1 0/0 +ERG 2078 mskcc.org GRCh38 21 38575698 38575698 + Translation_Start_Site SNP C C T MSK_T001 MSK_N001 C C c.3G>A p.Met1? p.M1? ENST00000442448 3/11 331 223 96 449 442 0 ERG,start_lost,p.Met1?,ENST00000442448,NM_004449.4;ERG,start_lost,p.Met1?,ENST00000417133,NM_001243432.2,NM_001136154.1;ERG,start_lost,p.Met1?,ENST00000398910,NM_001291391.1;ERG,start_lost,p.Met1?,ENST00000398911,;ERG,start_lost,p.Met1?,ENST00000398919,NM_001243428.1;ERG,5_prime_UTR_variant,,ENST00000398897,NM_001243429.1;ERG,non_coding_transcript_exon_variant,,ENST00000485493,;ERG,non_coding_transcript_exon_variant,,ENST00000468474,; T ENSG00000157554 ENST00000442448 Transcript start_lost 275/5034 3/1389 1/462 M/I atG/atA COSV67366082 1 -1 ERG HGNC HGNC:3446 protein_coding CCDS13657.1 ENSP00000394694 P11308.226 UPI0000046820 NM_004449.4 deleterious_low_confidence(0.01) benign(0.223) 3/11 AlphaFold_DB_import:AF-P11308-F1 1 HIGH SNV 5 1 1 . TCA . . 38575698 0/1 0/0 +TMPRSS2 7113 mskcc.org GRCh38 21 41479183 41479183 + Frame_Shift_Del DEL T T - novel MSK_T001 MSK_N001 T T c.672del p.Lys224AsnfsTer19 p.K224Nfs*19 ENST00000332149 7/14 512 435 77 695 695 0 TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000676973,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000679054,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000678348,;TMPRSS2,frameshift_variant,p.Lys277AsnfsTer19,ENST00000679263,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000332149,NM_005656.4;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000678171,NM_001382720.1;TMPRSS2,frameshift_variant,p.Lys155AsnfsTer19,ENST00000679016,;TMPRSS2,frameshift_variant,p.Lys261AsnfsTer19,ENST00000398585,NM_001135099.1;TMPRSS2,frameshift_variant,p.Lys116AsnfsTer19,ENST00000678743,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000454499,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000458356,;TMPRSS2,frameshift_variant,p.Lys184AsnfsTer19,ENST00000424093,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000678617,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer19,ENST00000679181,;TMPRSS2,frameshift_variant,p.Lys224AsnfsTer16,ENST00000677680,;TMPRSS2,3_prime_UTR_variant,,ENST00000678959,; - ENSG00000184012 ENST00000332149 Transcript frameshift_variant 806/3450 672/1479 224/492 K/X aaA/aa 1 -1 TMPRSS2 HGNC HGNC:11876 protein_coding YES CCDS33564.1 ENSP00000330330 O15393.205 UPI0000049921 NM_005656.4 7/14 PDB-ENSP_mappings:7meq.A,Pfam:PF15494,Gene3D:3.10.250.10,SMART:SM00202,Superfamily:SSF56487,PANTHER:PTHR24253,AlphaFold_DB_import:AF-O15393-F1 HIGH 1 deletion 1 1 . AGTT . . 41479182 0/1 0/0 +TMPRSS2 7113 mskcc.org GRCh38 21 41479219 41479219 + Silent SNP C C T MSK_T001 MSK_N001 C C c.636G>A p.Leu212= p.L212= ENST00000332149 7/14 1224 782 373 1044 996 0 TMPRSS2,synonymous_variant,p.Leu212=,ENST00000676973,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000679054,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000678348,;TMPRSS2,synonymous_variant,p.Leu265=,ENST00000679263,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000332149,NM_005656.4;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000678171,NM_001382720.1;TMPRSS2,synonymous_variant,p.Leu143=,ENST00000679016,;TMPRSS2,synonymous_variant,p.Leu249=,ENST00000398585,NM_001135099.1;TMPRSS2,synonymous_variant,p.Leu104=,ENST00000678743,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000454499,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000458356,;TMPRSS2,synonymous_variant,p.Leu172=,ENST00000424093,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000678617,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000679181,;TMPRSS2,synonymous_variant,p.Leu212=,ENST00000677680,;TMPRSS2,3_prime_UTR_variant,,ENST00000678959,; T ENSG00000184012 ENST00000332149 Transcript synonymous_variant 770/3450 636/1479 212/492 L ctG/ctA COSV106461584 1 -1 TMPRSS2 HGNC HGNC:11876 protein_coding YES CCDS33564.1 ENSP00000330330 O15393.205 UPI0000049921 NM_005656.4 7/14 PDB-ENSP_mappings:7meq.A,Pfam:PF15494,Gene3D:3.10.250.10,SMART:SM00202,Superfamily:SSF56487,PANTHER:PTHR24253,AlphaFold_DB_import:AF-O15393-F1 1 LOW 1 SNV 1 1 1 . TCA . . 41479219 0/1 0/0 +TMPRSS2 7113 mskcc.org GRCh38 21 41488494 41488494 + Missense_Mutation SNP G G T MSK_T001 MSK_N001 G G c.345C>A p.Asn115Lys p.N115K ENST00000332149 5/14 380 350 30 0 . . TMPRSS2,missense_variant,p.Asn115Lys,ENST00000676973,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000679054,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000678348,;TMPRSS2,missense_variant,p.Asn168Lys,ENST00000679263,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000332149,NM_005656.4;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000678171,NM_001382720.1;TMPRSS2,missense_variant,p.Asn152Lys,ENST00000398585,NM_001135099.1;TMPRSS2,missense_variant,p.Asn7Lys,ENST00000678743,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000454499,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000458356,;TMPRSS2,intron_variant,,ENST00000424093,;TMPRSS2,intron_variant,,ENST00000679016,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000678617,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000463138,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000679181,;TMPRSS2,missense_variant,p.Asn115Lys,ENST00000677680,;TMPRSS2,3_prime_UTR_variant,,ENST00000678959,; T ENSG00000184012 ENST00000332149 Transcript missense_variant 479/3450 345/1479 115/492 N/K aaC/aaA COSV59825472 1 -1 TMPRSS2 HGNC HGNC:11876 protein_coding YES CCDS33564.1 ENSP00000330330 O15393.205 UPI0000049921 NM_005656.4 tolerated(0.84) benign(0.013) 5/14 PDB-ENSP_mappings:7meq.A,CDD:cd00112,Gene3D:4.10.400.10,SMART:SM00192,Superfamily:SSF57424,PROSITE_profiles:PS50068,AlphaFold_DB_import:AF-O15393-F1 1 MODERATE 1 SNV 1 1 1 . AGT . . 41488494 0/1 0/0 +TMPRSS2 7113 mskcc.org GRCh38 21 41494550 41494550 + Missense_Mutation SNP T T C rs774327563 MSK_T001 MSK_N001 T T c.44A>G p.Tyr15Cys p.Y15C ENST00000332149 3/14 356 260 96 781 781 0 TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000676973,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000679054,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000678348,;TMPRSS2,missense_variant,p.Tyr68Cys,ENST00000679263,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000332149,NM_005656.4;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000678171,NM_001382720.1;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000679016,;TMPRSS2,missense_variant,p.Tyr52Cys,ENST00000398585,NM_001135099.1;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000454499,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000458356,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000424093,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000455813,;TMPRSS2,intron_variant,,ENST00000678743,;TMPRSS2,non_coding_transcript_exon_variant,,ENST00000678617,;TMPRSS2,intron_variant,,ENST00000463138,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000679181,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000677680,;TMPRSS2,missense_variant,p.Tyr15Cys,ENST00000678959,; C ENSG00000184012 ENST00000332149 Transcript missense_variant 178/3450 44/1479 15/492 Y/C tAt/tGt rs774327563 1 -1 TMPRSS2 HGNC HGNC:11876 protein_coding YES CCDS33564.1 ENSP00000330330 O15393.205 UPI0000049921 NM_005656.4 deleterious(0.01) benign(0.022) 3/14 AlphaFold_DB_import:AF-O15393-F1 MODERATE 1 SNV 1 1 . ATA . . 1.995e-05 0.0001232 5.444e-05 1.762e-05 5 41494550 0/1 0/0 +UMODL1 89766 mskcc.org GRCh38 21 42085325 42085325 + Silent SNP C C T rs185422923 MSK_T001 MSK_N001 C C c.516C>T p.Asn172= p.N172= ENST00000408910 4/23 366 193 173 0 . . UMODL1,synonymous_variant,p.Asn100=,ENST00000400424,NM_001199528.4;UMODL1,synonymous_variant,p.Asn100=,ENST00000400427,NM_001199527.3;UMODL1,synonymous_variant,p.Asn172=,ENST00000408989,NM_173568.4;UMODL1,synonymous_variant,p.Asn172=,ENST00000408910,NM_001004416.3;UMODL1,synonymous_variant,p.Asn8=,ENST00000491559,;UMODL1,synonymous_variant,p.Asn8=,ENST00000466434,;UMODL1,synonymous_variant,p.Asn8=,ENST00000400421,;UMODL1,synonymous_variant,p.Asn8=,ENST00000468982,;UMODL1,synonymous_variant,p.Asn8=,ENST00000485357,;UMODL1,synonymous_variant,p.Asn8=,ENST00000497243,; T ENSG00000177398 ENST00000408910 Transcript synonymous_variant 516/4879 516/3957 172/1318 N aaC/aaT rs185422923 1 1 UMODL1 HGNC HGNC:12560 protein_coding YES CCDS42936.1 ENSP00000386147 Q5DID0.147 UPI00006C2192 NM_001004416.3 4/23 AlphaFold_DB_import:AF-Q5DID0-F1 0.0002 0.0008 LOW 1 SNV 1 . ACG . . 8.016e-06 6.457e-05 3.268e-05 2 42085325 0/1 0/0 +U2AF1 7307 mskcc.org GRCh38 21 43093128 43093128 + Missense_Mutation SNP C C T novel MSK_T001 MSK_N001 C C c.697G>A p.Asp233Asn p.D233N ENST00000291552 8/8 454 425 29 344 344 0 U2AF1,missense_variant,p.Asp160Asn,ENST00000459639,NM_001025204.2;U2AF1,missense_variant,p.Asp233Asn,ENST00000291552,NM_006758.3;U2AF1,missense_variant,p.Asp233Asn,ENST00000380276,NM_001025203.1;U2AF1,3_prime_UTR_variant,,ENST00000464750,;U2AF1,non_coding_transcript_exon_variant,,ENST00000475639,;U2AF1,non_coding_transcript_exon_variant,,ENST00000478282,;U2AF1,non_coding_transcript_exon_variant,,ENST00000471250,;U2AF1,downstream_gene_variant,,ENST00000463599,;U2AF1,downstream_gene_variant,,ENST00000486519,;U2AF1,downstream_gene_variant,,ENST00000496462,; T ENSG00000160201 ENST00000291552 Transcript missense_variant 773/945 697/723 233/240 D/N Gat/Aat 1 -1 U2AF1 HGNC HGNC:12453 protein_coding YES CCDS13694.1 ENSP00000291552 Q01081.241 UPI0000000C26 NM_006758.3 tolerated_low_confidence(0.09) unknown(0) 8/8 Low_complexity_(Seg):seg,PANTHER:PTHR12620,MobiDB_lite:mobidb-lite,MobiDB_lite:mobidb-lite,AlphaFold_DB_import:AF-Q01081-F1 MODERATE 1 SNV 1 1 . TCT . . 43093128 0/1 0/0 +U2AF1 7307 mskcc.org GRCh38 21 43104375 43104375 + Silent SNP A A G rs755067307 MSK_T001 MSK_N001 A A c.72T>C p.Ile24= p.I24= ENST00000291552 2/8 667 607 60 0 . . U2AF1,synonymous_variant,p.Ile24=,ENST00000291552,NM_006758.3;U2AF1,synonymous_variant,p.Ile24=,ENST00000380276,NM_001025203.1;U2AF1,5_prime_UTR_variant,,ENST00000459639,NM_001025204.2;,upstream_gene_variant,,ENST00000668861,;U2AF1,synonymous_variant,p.Ile24=,ENST00000464750,;U2AF1,synonymous_variant,p.Ile24=,ENST00000486519,;U2AF1,non_coding_transcript_exon_variant,,ENST00000475639,;U2AF1,non_coding_transcript_exon_variant,,ENST00000496462,;U2AF1,non_coding_transcript_exon_variant,,ENST00000463599,;U2AF1,upstream_gene_variant,,ENST00000468039,;,regulatory_region_variant,,ENSR00001365846,; G ENSG00000160201 ENST00000291552 Transcript synonymous_variant 148/945 72/723 24/240 I atT/atC rs755067307 1 -1 U2AF1 HGNC HGNC:12453 protein_coding YES CCDS13694.1 ENSP00000291552 Q01081.241 UPI0000000C26 NM_006758.3 2/8 PROSITE_profiles:PS50103,PANTHER:PTHR12620,Pfam:PF00642,SMART:SM00356,Prints:PR01848,AlphaFold_DB_import:AF-Q01081-F1 LOW 1 SNV 1 1 . CAA . . 7.992e-06 2.921e-05 8.823e-06 2 43104375 0/1 0/0 +SIK1 150094 mskcc.org GRCh38 21 43419117 43419117 + Missense_Mutation SNP C C T novel MSK_T001 MSK_N001 C C c.1366G>A p.Glu456Lys p.E456K ENST00000270162 11/14 113 . 45 0 . . SIK1,missense_variant,p.Glu456Lys,ENST00000270162,NM_173354.5;SIK1,downstream_gene_variant,,ENST00000644750,;SIK1,downstream_gene_variant,,ENST00000478426,;SIK1,downstream_gene_variant,,ENST00000644689,;SIK1,downstream_gene_variant,,ENST00000644871,; T ENSG00000142178 ENST00000270162 Transcript missense_variant 1502/4747 1366/2352 456/783 E/K Gag/Aag 1 -1 SIK1 HGNC HGNC:11142 protein_coding YES CCDS33575.1 ENSP00000270162 P57059.208 UPI0000206F2B NM_173354.5 deleterious(0.03) possibly_damaging(0.505) 11/14 PIRSF:PIRSF037014,MobiDB_lite:mobidb-lite,AlphaFold_DB_import:AF-P57059-F1 MODERATE 1 SNV 1 1 . TCC . . 43419117 0/1 0/0 +ICOSLG 23308 mskcc.org GRCh38 21 44235374 44235374 + Missense_Mutation SNP C C A MSK_T001 MSK_N001 C C c.595G>T p.Val199Leu p.V199L ENST00000407780 4/7 101 88 13 153 153 0 ICOSLG,missense_variant,p.Val199Leu,ENST00000407780,NM_015259.6;ICOSLG,missense_variant,p.Val199Leu,ENST00000400379,;ICOSLG,missense_variant,p.Val199Leu,ENST00000643466,;ICOSLG,missense_variant,p.Val199Leu,ENST00000700361,;ICOSLG,missense_variant,p.Val82Leu,ENST00000400377,NM_001283051.2;ICOSLG,missense_variant,p.Val158Leu,ENST00000700352,;ICOSLG,missense_variant,p.Val199Leu,ENST00000700355,NM_001395918.1;ICOSLG,missense_variant,p.Val114Leu,ENST00000700358,NM_001283052.2,NM_001365759.2;ICOSLG,missense_variant,p.Val199Leu,ENST00000344330,NM_001283050.2;ICOSLG,missense_variant,p.Val114Leu,ENST00000700360,;ICOSLG,3_prime_UTR_variant,,ENST00000700350,;ICOSLG,3_prime_UTR_variant,,ENST00000700356,;ICOSLG,3_prime_UTR_variant,,ENST00000700357,;ICOSLG,3_prime_UTR_variant,,ENST00000700359,;ICOSLG,non_coding_transcript_exon_variant,,ENST00000700354,;ICOSLG,non_coding_transcript_exon_variant,,ENST00000700351,;ICOSLG,non_coding_transcript_exon_variant,,ENST00000700353,; A ENSG00000160223 ENST00000407780 Transcript missense_variant 721/7078 595/909 199/302 V/L Gtg/Ttg COSV60266097 1 -1 ICOSLG HGNC HGNC:17087 protein_coding YES CCDS42952.1 ENSP00000384432 O75144.200 A0N0L8.135 UPI0000049DCB NM_015259.6 deleterious(0) possibly_damaging(0.807) 4/7 Gene3D:2.60.40.10,PDB-ENSP_mappings:6x4g.C,PDB-ENSP_mappings:6x4t.A,PDB-ENSP_mappings:6x4t.C,AlphaFold_DB_import:AF-O75144-F1,PROSITE_profiles:PS50835,PANTHER:PTHR24100,Superfamily:SSF48726 1 MODERATE 1 SNV 1 1 . ACG . . 44235374 0/1 0/0 +ICOSLG 23308 mskcc.org GRCh38 21 44236903 44236903 + Missense_Mutation SNP C C T novel MSK_T001 MSK_N001 C C c.370G>A p.Glu124Lys p.E124K ENST00000407780 3/7 950 827 123 630 629 1 ICOSLG,missense_variant,p.Glu124Lys,ENST00000407780,NM_015259.6;ICOSLG,missense_variant,p.Glu124Lys,ENST00000400379,;ICOSLG,missense_variant,p.Glu124Lys,ENST00000643466,;ICOSLG,missense_variant,p.Glu124Lys,ENST00000700361,;ICOSLG,missense_variant,p.Glu83Lys,ENST00000700352,;ICOSLG,missense_variant,p.Glu124Lys,ENST00000700355,NM_001395918.1;ICOSLG,missense_variant,p.Glu39Lys,ENST00000700358,NM_001283052.2,NM_001365759.2;ICOSLG,missense_variant,p.Glu124Lys,ENST00000344330,NM_001283050.2;ICOSLG,missense_variant,p.Glu39Lys,ENST00000700360,;ICOSLG,intron_variant,,ENST00000400377,NM_001283051.2;,upstream_gene_variant,,ENST00000619053,;ICOSLG,missense_variant,p.Gly73Glu,ENST00000700359,;ICOSLG,3_prime_UTR_variant,,ENST00000700350,;ICOSLG,3_prime_UTR_variant,,ENST00000700356,;ICOSLG,3_prime_UTR_variant,,ENST00000700357,;ICOSLG,non_coding_transcript_exon_variant,,ENST00000700354,;ICOSLG,non_coding_transcript_exon_variant,,ENST00000700351,;ICOSLG,non_coding_transcript_exon_variant,,ENST00000700353,; T ENSG00000160223 ENST00000407780 Transcript missense_variant 496/7078 370/909 124/302 E/K Gag/Aag 1 -1 ICOSLG HGNC HGNC:17087 protein_coding YES CCDS42952.1 ENSP00000384432 O75144.200 A0N0L8.135 UPI0000049DCB NM_015259.6 tolerated(1) benign(0.003) 3/7 Gene3D:2.60.40.10,PDB-ENSP_mappings:6x4g.C,PDB-ENSP_mappings:6x4t.A,PDB-ENSP_mappings:6x4t.C,AlphaFold_DB_import:AF-O75144-F1,Pfam:PF07686,PROSITE_profiles:PS50835,PANTHER:PTHR24100,SMART:SM00409,Superfamily:SSF48726,CDD:cd20935 MODERATE 1 SNV 1 . TCC . . 44236903 0/1 0/0 +ICOSLG 23308 mskcc.org GRCh38 21 44237111 44237111 + Nonsense_Mutation SNP C C T novel MSK_T001 MSK_N001 C C c.162G>A p.Trp54Ter p.W54* ENST00000407780 3/7 944 745 199 596 596 0 ICOSLG,stop_gained,p.Trp54Ter,ENST00000407780,NM_015259.6;ICOSLG,stop_gained,p.Trp54Ter,ENST00000400379,;ICOSLG,stop_gained,p.Trp54Ter,ENST00000643466,;ICOSLG,stop_gained,p.Trp54Ter,ENST00000700361,;ICOSLG,stop_gained,p.Trp54Ter,ENST00000700355,NM_001395918.1;ICOSLG,stop_gained,p.Trp54Ter,ENST00000344330,NM_001283050.2;ICOSLG,5_prime_UTR_variant,,ENST00000700358,NM_001283052.2,NM_001365759.2;ICOSLG,intron_variant,,ENST00000400377,NM_001283051.2;ICOSLG,intron_variant,,ENST00000700352,;ICOSLG,intron_variant,,ENST00000700360,;,upstream_gene_variant,,ENST00000619053,;ICOSLG,3_prime_UTR_variant,,ENST00000700350,;ICOSLG,3_prime_UTR_variant,,ENST00000700356,;ICOSLG,3_prime_UTR_variant,,ENST00000700357,;ICOSLG,non_coding_transcript_exon_variant,,ENST00000700354,;ICOSLG,non_coding_transcript_exon_variant,,ENST00000700351,;ICOSLG,intron_variant,,ENST00000700359,;ICOSLG,upstream_gene_variant,,ENST00000700353,;,regulatory_region_variant,,ENSR00001237806,; T ENSG00000160223 ENST00000407780 Transcript stop_gained 288/7078 162/909 54/302 W/* tgG/tgA 1 -1 ICOSLG HGNC HGNC:17087 protein_coding YES CCDS42952.1 ENSP00000384432 O75144.200 A0N0L8.135 UPI0000049DCB NM_015259.6 3/7 Gene3D:2.60.40.10,PDB-ENSP_mappings:6x4g.C,PDB-ENSP_mappings:6x4t.A,PDB-ENSP_mappings:6x4t.C,AlphaFold_DB_import:AF-O75144-F1,Pfam:PF07686,PROSITE_profiles:PS50835,PANTHER:PTHR24100,SMART:SM00409,Superfamily:SSF48726,CDD:cd20935 HIGH 1 SNV 1 . GCC . . 44237111 0/1 0/0 diff --git a/tests/vcf2maf.t b/tests/vcf2maf.t index e0f4d1a..d5da0a2 100644 --- a/tests/vcf2maf.t +++ b/tests/vcf2maf.t @@ -16,12 +16,12 @@ ok( system( "docker run --rm vcf2maf:main perl vcf2maf.pl --help > /dev/null" ) ok( system( "docker run --rm vcf2maf:main perl vcf2maf.pl --man > /dev/null" ) == 0 ); # Test standard operation, diff, and cleanup -ok( system( "docker run --rm -v $test_dir:/opt/tests vcf2maf:main perl vcf2maf.pl --vep-path /usr/local/bin --vep-data tests --ncbi-build GRCh38 --input-vcf tests/test_b38.vcf --output-maf tests/test_b38_output.new.maf --ref-fasta tests/Homo_sapiens.GRCh38.dna.chromosome.21.fa" ) == 0 ); +ok( system( "docker run --rm -v $test_dir:/opt/tests vcf2maf:main perl vcf2maf.pl --vep-path /usr/local/bin --vep-data tests --vep-overwrite --ncbi-build GRCh38 --input-vcf tests/test_b38.vcf --output-maf tests/test_b38_output.new.maf --ref-fasta tests/Homo_sapiens.GRCh38.dna.chromosome.21.fa" ) == 0 ); # Skip column 76 (DOMAINS) in the diff, since it is a randomly ordered comma-delimited list ok( system( "bash -c 'diff <(cut -f1-75,77- tests/test_b38_output.maf) <(cut -f1-75,77- tests/test_b38_output.new.maf)'" ) == 0 ); system( "rm -f tests/test_b38_output.new.maf" ); # Test some more options, diff, and cleanup -ok( system( "docker run --rm -v $test_dir:/opt/tests vcf2maf:main perl vcf2maf.pl --vep-path /usr/local/bin --vep-data tests --ncbi-build GRCh38 --input-vcf tests/test_b38.vcf --output-maf tests/test_b38_output.more.new.maf --ref-fasta tests/Homo_sapiens.GRCh38.dna.chromosome.21.fa --vep-overwrite --vcf-tumor-id TUMOR --vcf-normal-id NORMAL --tumor-id MSK_T001 --normal-id MSK_N001 --maf-center mskcc.org --vep-forks 1 --buffer-size 50 --vep-custom tests/test_b38.gnomad.exomes.r2.1.1.sites.vcf.gz,gnomAD,vcf,exact,,AC --retain-ann gnomAD_AC --retain-fmt GT" ) == 0 ); +ok( system( "docker run --rm -v $test_dir:/opt/tests vcf2maf:main perl vcf2maf.pl --vep-path /usr/local/bin --vep-data tests --vep-overwrite --vep-forks 1 --ncbi-build GRCh38 --input-vcf tests/test_b38.vcf --output-maf tests/test_b38_output.more.new.maf --ref-fasta tests/Homo_sapiens.GRCh38.dna.chromosome.21.fa --vcf-tumor-id TUMOR --vcf-normal-id NORMAL --tumor-id MSK_T001 --normal-id MSK_N001 --maf-center mskcc.org --buffer-size 50 --vep-custom tests/test_b38.gnomad.exomes.r2.1.1.sites.vcf.gz,gnomAD,vcf,exact,,AC --retain-ann gnomAD_AC --retain-fmt GT" ) == 0 ); ok( system( "bash -c 'diff <(cut -f1-75,77- tests/test_b38_output.more.maf) <(cut -f1-75,77- tests/test_b38_output.more.new.maf)'" ) == 0 ); system( "rm -f tests/test_b38_output.more.new.maf tests/test_b38.vep.vcf" ); diff --git a/vcf2maf.pl b/vcf2maf.pl index 319c408..46cd409 100755 --- a/vcf2maf.pl +++ b/vcf2maf.pl @@ -15,7 +15,7 @@ # Set any default paths and constants my ( $tumor_id, $normal_id ) = ( "TUMOR", "NORMAL" ); my ( $vep_path, $vep_data, $vep_forks, $buffer_size, $any_allele, $inhibit_vep, $online, $vep_custom, $vep_config, $vep_overwrite, $vep_stats ) = ( "$ENV{HOME}/miniconda3/bin", "$ENV{HOME}/.vep", 4, 5000, 0, 0, 0, "", "", 0 , 0); -my ( $ref_fasta ) = ( "$ENV{HOME}/.vep/homo_sapiens/102_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz" ); +my ( $ref_fasta ) = ( "$ENV{HOME}/.vep/homo_sapiens/112_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz" ); my ( $species, $ncbi_build, $cache_version, $maf_center, $retain_info, $retain_fmt, $retain_ann, $min_hom_vaf, $max_subpop_af ) = ( "homo_sapiens", "GRCh37", "", ".", "", "", "", 0.7, 0.0004 ); my $perl_bin = $Config{perlpath}; @@ -143,6 +143,7 @@ sub GetBiotypePriority { 'regulatory_region' => 6, # A region of sequence that is involved in the control of a biological process 'disrupted_domain' => 6, # Otherwise viable coding region omitted from this alternatively spliced transcript because the splice variation affects a region coding for a protein domain 'processed_transcript' => 6, # Doesn't contain an ORF + 'protein_coding_CDS_not_defined' => 6, # Transcript that belongs to a protein_coding gene and doesn't contain an ORF. Replaces the processed_transcript transcript biotype in protein_coding genes 'TEC' => 6, # To be Experimentally Confirmed. This is used for non-spliced EST clusters that have polyA features. This category has been specifically created for the ENCODE project to highlight regions that could indicate the presence of protein coding genes that require experimental validation, either by 5' RACE or RT-PCR to extend the transcripts, or by confirming expression of the putatively-encoded peptide with specific antibodies 'TF_binding_site' => 7, # A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex 'CTCF_binding_site' =>7, # A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor @@ -517,8 +518,9 @@ sub GetBiotypePriority { SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS AF AFR_AF AMR_AF ASN_AF EAS_AF EUR_AF SAS_AF AA_AF EA_AF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL - HGVS_OFFSET PHENO MINIMISED GENE_PHENO FILTER flanking_bps vcf_id vcf_qual gnomAD_AF gnomAD_AFR_AF - gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF ); + HGVS_OFFSET PHENO MINIMISED GENE_PHENO FILTER flanking_bps vcf_id vcf_qual gnomADe_AF gnomADe_AFR_AF + gnomADe_AMR_AF gnomADe_ASJ_AF gnomADe_EAS_AF gnomADe_FIN_AF gnomADe_NFE_AF gnomADe_OTH_AF gnomADe_SAS_AF +); # push any requested custom VEP annotations from the CSQ/ANN section into @ann_cols if ($retain_ann) { @@ -888,8 +890,8 @@ sub GetBiotypePriority { # Copy FILTER from input VCF, and tag calls with high allele freq in any gnomAD subpopulation my $subpop_count = 0; foreach my $subpop ( qw( AFR AMR ASJ EAS FIN NFE SAS )) { - if( $maf_line{"gnomAD_$subpop\_AF"} ) { - my ( $subpop_af ) = split( "/", $maf_line{"gnomAD_$subpop\_AF"} ); + if( $maf_line{"gnomADe_$subpop\_AF"} ) { + my ( $subpop_af ) = split( "/", $maf_line{"gnomADe_$subpop\_AF"} ); $subpop_count++ if( $subpop_af > $max_subpop_af ); } } @@ -1200,7 +1202,7 @@ =head1 OPTIONS =item B<--ref-fasta>=I -Reference FASTA file [~/.vep/homo_sapiens/102_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz] +Reference FASTA file [~/.vep/homo_sapiens/112_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz] =item B<--species>=I @@ -1212,7 +1214,7 @@ =head1 OPTIONS =item B<--cache-version>=I -Version of offline cache to use with VEP (e.g. 75, 91, 102) [Default: Installed version] +Version of offline cache to use with VEP (e.g. 75, 91, 112) [Default: Installed version] =item B<--remap-chain>=I @@ -1402,8 +1404,6 @@ =head2 RELEVANT LINKS: =head1 AUTHORS Cyriac Kandoth (ckandoth@gmail.com) - Shweta Chavan (chavan.shweta@gmail.com) - Zuojian Tang (zuojian.tang@gmail.com) =head1 LICENSE diff --git a/vcf2vcf.pl b/vcf2vcf.pl index 30396bb..f5176e8 100644 --- a/vcf2vcf.pl +++ b/vcf2vcf.pl @@ -42,7 +42,7 @@ # Parse options and print usage if there is a syntax error, or if usage was explicitly requested my ( $man, $help, $add_filters ) = ( 0, 0, 0 ); my ( $input_vcf, $output_vcf, $new_tumor_id, $new_normal_id, $remap_chain ); -my ( $tumor_bam, $normal_bam, $ref_fasta ) = ( "", "", "$ENV{HOME}/.vep/homo_sapiens/102_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz" ); +my ( $tumor_bam, $normal_bam, $ref_fasta ) = ( "", "", "$ENV{HOME}/.vep/homo_sapiens/112_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz" ); GetOptions( 'help!' => \$help, 'man!' => \$man, @@ -486,7 +486,7 @@ =head1 OPTIONS --new-normal-id Matched normal ID to use in the new VCF [--vcf-normal-id] --tumor-bam Path to tumor BAM, if provided, will add or override DP:AD:ADF:ADR in output VCF --normal-bam Path to normal BAM, if provided, will add or override DP:AD:ADF:ADR in output VCF - --ref-fasta Reference FASTA file [~/.vep/homo_sapiens/102_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz] + --ref-fasta Reference FASTA file [~/.vep/homo_sapiens/112_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz] --add-header VCF-style header lines to add to the output VCF; Use "\n" to separate lines [] --add-info Comma-delimited tag=value pairs to add as INFO fields in the output VCF [] --retain-info Comma-delimited names of INFO fields to retain in output VCF [SOMATIC,SS,I16,MQSB]