3-14145982-T-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004628.5(XPC):c.2782A>C(p.Lys928Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000478 in 1,608,788 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004628.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XPC | ENST00000285021.12 | c.2782A>C | p.Lys928Gln | missense_variant | Exon 16 of 16 | 1 | NM_004628.5 | ENSP00000285021.8 | ||
ENSG00000268279 | ENST00000608606.1 | n.*198+299T>G | intron_variant | Intron 4 of 4 | 5 | ENSP00000476275.1 |
Frequencies
GnomAD3 genomes AF: 0.00261 AC: 396AN: 151990Hom.: 1 Cov.: 28
GnomAD3 exomes AF: 0.000563 AC: 140AN: 248832Hom.: 1 AF XY: 0.000430 AC XY: 58AN XY: 135034
GnomAD4 exome AF: 0.000255 AC: 372AN: 1456680Hom.: 2 Cov.: 37 AF XY: 0.000242 AC XY: 175AN XY: 723636
GnomAD4 genome AF: 0.00261 AC: 397AN: 152108Hom.: 1 Cov.: 28 AF XY: 0.00239 AC XY: 178AN XY: 74382
ClinVar
Submissions by phenotype
Xeroderma pigmentosum, group C Benign:2
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -
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Xeroderma pigmentosum Benign:1
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not provided Benign:1
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XPC-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not specified Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at