CHR POS REF OBS ALLELE BUILD CLINICAL_SIGNIFICANCE

Transcription

1 CHR POS REF OBS ALLELE BUILD CLINICAL_SIGNIFICANCE is_clinical dbsnp MITO GENE chr G C heterozygous DDX11L1 chr A G Homozygous rs ISG15 chr A G heterozygous rs C1orf159 chr A AC heterozygous clinical rs ABCA4 chr T - Homozygous rs HRNR chr C CAGCTCT heterozygous rs LCE4A chr A G heterozygous 36 probable-pathogenic clinical rs699 mito AGT chr T C heterozygous AGAP11;AGAP11,BC chr G C heterozygous SMG6 1 CHR Name of the reference contig/chromosome where the variant occurs 2 POS Position in the reference contig/chromosome where the variant occurs 3 REF Reference base at the variant site 4 OBS Observed/alternate base in the samples at the variant site 5 ALLELE Genotype of the sample. Genotypes: homozygous and heterozygous 6 BUILD Gene ID associated with the locaation of the variant call 7 CLINICAL_SIGNIFICANCE SNP clinical significance. Possible values are unknown, non-pathogenic,probable-nonpathogenic, probable-patogenic, pathogenic, drug-response, histocompatibility, other. Information from dbsnp 8 is_clinical SNP is clinical. Information from dbsnp 9 dbsnp dbsnp identifier. If the observed variant exists in the dbsnp the rs identifier is shown 10 MITO If protein is predicted to target the mitochondria 11 GENE Gene ID associated with the location of the variant call

2 DESCRIPTION VARIANT_FUNC TION EXONIC_FUNCTION AA_CHANGES AA_CHANGE - ncrna_exonic Ubiquitin-like protein ISG15 exonic synonymous ISG15:uc001acj.3:exon2:c.A294G:p.V98V, V => V Uncharacterized protein C1orf159 exonic synonymous C1orf159:uc001acn.2:exon5:c.T357C:p.I119I,C1or I => I Retinal-specific ATP-binding cassette transporter intronic Hornerin exonic frameshift deletion HRNR:uc001ezt.1:exon2:c.1delA:p.M1fs, - Late cornified envelope protein 4A exonic nonframeshift substitution LCE4A:uc001fak.2:exon1:c.129_129delinsCAGCTC TGGGGGCTGCTGT, - Angiotensinogen exonic nonsynonymous AGT:uc009xff.2:exon3:c.T719C:p.M240T,AGT:uc0 M => T Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 11 exonic;splicing nonsynonymous AGAP11:uc009xnf.2:exon4:c.A395G:p.H132R, H => R Telomerase-binding protein EST1A exonic nonsynonymous SMG6:uc010vqv.1:exon5:c.C569G:p.S190W,SMG 6:uc002fub.1:exon13:c.C3293G:p.S1098W, S => W 12 DESCRIPTION Gene ID description VARIANT_FUNCT ION EXONIC_FUNCTI ON Annotation of the variant with respect to its genomic context. Possible annotations are exonic, UTR5, UTR3, intronic, intergenic, splicing, downstream, upstream. When several protein splice variants overlap Annotation of the functional class of the variant. Possible annotations are synonymous, nonsynonymous, framshift deletion, frameshift substitution 15 AA_CHANGES Aminoacid change produced in the different transcripts. c = cdna, p = protein 16 AA_CHANGE Aminoacid change produced: REFERENCE => MUTATION

3 SIFT PP2 LRT OMIM OMIM_DESC PATHWAY GO GO_DESC UBIQUITIN-LIKE RIG-I-like receptor signaling GO: protein binding GO: membrane integral to ,601718, STARGARDT DISEASE 1; ABC transporters GO: nucleotide binding cornified envelope GO: LATE CORNIFIED - GO: keratinization tolerated benign neutral ANGIOTENSINOGEN; Hypertrophic cardiomyopathy GO: ovarian follicle rupture damaging GO: ARF GTPase activator damaging probably damaging deleterius SMG6, C. ELEGANS, - GO: nuclear-transcribed COLUMN NAME COLUMN NAME 17 SIFT 18 PP2 19 LRT Prediction whether the aminoacid substitution affects protein function. SIFT is based on the degree of cosnervation of aminoa amino acid residues in sequence alignments derived from closely related sequences. Possible values are tolater, damaging Prediction of the possible impact of the amino acid substitution on the structure and function of the protein using straightforward physical and comparative considerations. Possible values are probably damaging, possibly damaging and benign Prediction of deletetious mutations that disrupt highly conserved amino acid residues through a likelihood ratio test. Possible values are deleterious, neutral and unknown 20 OMIM OMIM IDs that are related to the corresponding gene. Information from the OMIM database 21 OMIM_DESC Description of the OMIM Ids 22 PATHWAY Functional pathway to which the corresponding gene belongs to. Information taken from the KEGG pathway database 23 GO Gene ontology IDs that are related to the correspondin gene. Information from GO.org 24 GO_DESC Description of the GO Ids

4 CONSERVE D SCORE FILTER DP A C G T conserved StdFilter PASS conserved PASS StdFilter conserved StdFilter PASS PASS conserved StdFilter conserved PASS CONSERVED Conserved elements produce by the phastcons program based on a whole-genome alignment of 46 vertebrates. Information taken from UCSC 26 SCORE Probability that REF/ALT polymorphism exists at this site given the sequencing data. In phred scale 27 FILTER Default filters for SNPs: StdFilter (QUAL<50.0 AB >0.75 FS > QD < 5.0 HRun > 5.0), LowD (DP < 6.0), Hard2Validate (MQ0 >= 4.0 && MQ0/DP> 0.1) Default filters for Indels: StdFilter (QUAL<50.0 FS > QD < 2.0), LowD (DP <6 ) Variant passing the default filters will be tagged as PASS 28 DP Total depth of reads 29 A A s observed at the variant position 30 C C s observed at the variant position 31 G G s observed at the variant position 32 T T s observed at the variant position FS QD MQ AB GT GQ LKH /1 99 0:1:0

5 /1 99 0:0: /1 99 0:1: /1 99 0:1: /1 99 0:0: /1 99 0:1: /1 99 0:1: /1 99 0:1: /1 99 0:1:0 33 FS Strand Bias. Evidence for the variation of the reads to be seen only on the forward or only in te reverse strand. Higher values denote more bias and therfore are more likely to indicate fasle positive calls 34 QD Quality by depth. Variant confidence. Low scores are indicative of fals positive calls and artifacts 35 MQ Mapping quality 36 AB Allele balance of REF/ALT in heterozygous 37 GT The genotype of this sample. Possible values are heterozygous (0/1: 1 REF and 1 ALT) and homozygous (1/1: 2 ALT alleles) 38 GQ Genotype quality. In Phred scale 39 LKH Likelihoods of the 3 genotypes.