rs375859472
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004628.5(XPC):c.2621C>T(p.Pro874Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,608,990 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_004628.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
XPC | NM_004628.5 | c.2621C>T | p.Pro874Leu | missense_variant | 16/16 | ENST00000285021.12 | NP_004619.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XPC | ENST00000285021.12 | c.2621C>T | p.Pro874Leu | missense_variant | 16/16 | 1 | NM_004628.5 | ENSP00000285021.8 | ||
ENSG00000268279 | ENST00000608606.1 | n.*198+460G>A | intron_variant | 5 | ENSP00000476275.1 |
Frequencies
GnomAD3 genomes AF: 0.0000660 AC: 10AN: 151610Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.00000828 AC: 2AN: 241544Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131386
GnomAD4 exome AF: 0.00000549 AC: 8AN: 1457380Hom.: 0 Cov.: 37 AF XY: 0.00000552 AC XY: 4AN XY: 724868
GnomAD4 genome AF: 0.0000660 AC: 10AN: 151610Hom.: 0 Cov.: 28 AF XY: 0.0000811 AC XY: 6AN XY: 73986
ClinVar
Submissions by phenotype
Xeroderma pigmentosum, group C Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Oct 09, 2017 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at