rs587778757
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004628.5(XPC):c.52A>C(p.Ser18Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,524 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S18S) has been classified as Likely benign.
Frequency
Consequence
NM_004628.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XPC | NM_004628.5 | c.52A>C | p.Ser18Arg | missense_variant | 1/16 | ENST00000285021.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XPC | ENST00000285021.12 | c.52A>C | p.Ser18Arg | missense_variant | 1/16 | 1 | NM_004628.5 | P1 | |
XPC | ENST00000476581.6 | c.52A>C | p.Ser18Arg | missense_variant, NMD_transcript_variant | 1/15 | 1 | |||
XPC | ENST00000511155.1 | c.52A>C | p.Ser18Arg | missense_variant | 1/4 | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460524Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726584
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Xeroderma pigmentosum, group C Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Dec 27, 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