3-14145808-C-T
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_004628.5(XPC):c.*133G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.001 in 1,145,242 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00054 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 16 hom. )
Consequence
XPC
NM_004628.5 3_prime_UTR
NM_004628.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.294
Genes affected
XPC (HGNC:12816): (XPC complex subunit, DNA damage recognition and repair factor) The protein encoded by this gene is a key component of the XPC complex, which plays an important role in the early steps of global genome nucleotide excision repair (NER). The encoded protein is important for damage sensing and DNA binding, and shows a preference for single-stranded DNA. Mutations in this gene or some other NER components can result in Xeroderma pigmentosum, a rare autosomal recessive disorder characterized by increased sensitivity to sunlight with the development of carcinomas at an early age. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 3-14145808-C-T is Benign according to our data. Variant chr3-14145808-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 343559.We mark this variant Likely_benign, oryginal submissions are: {Benign=1, Likely_benign=1, Uncertain_significance=1}.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000538 (82/152288) while in subpopulation SAS AF= 0.0158 (76/4822). AF 95% confidence interval is 0.0129. There are 1 homozygotes in gnomad4. There are 56 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 16 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
XPC | NM_004628.5 | c.*133G>A | 3_prime_UTR_variant | 16/16 | ENST00000285021.12 | NP_004619.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XPC | ENST00000285021 | c.*133G>A | 3_prime_UTR_variant | 16/16 | 1 | NM_004628.5 | ENSP00000285021.8 | |||
ENSG00000268279 | ENST00000608606.1 | n.*198+125C>T | intron_variant | 5 | ENSP00000476275.1 |
Frequencies
GnomAD3 genomes AF: 0.000545 AC: 83AN: 152170Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00224 AC: 346AN: 154570Hom.: 3 AF XY: 0.00294 AC XY: 244AN XY: 83032
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GnomAD4 exome AF: 0.00107 AC: 1063AN: 992954Hom.: 16 Cov.: 13 AF XY: 0.00154 AC XY: 781AN XY: 505844
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GnomAD4 genome AF: 0.000538 AC: 82AN: 152288Hom.: 1 Cov.: 32 AF XY: 0.000752 AC XY: 56AN XY: 74450
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:2
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Xeroderma pigmentosum Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Arrhythmogenic right ventricular cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Xeroderma pigmentosum, group C Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at