rs1805160
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_000380.4(XPA):c.683G>A(p.Arg228Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000172 in 1,613,702 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 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. R228R) has been classified as Likely benign.
Frequency
Consequence
NM_000380.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XPA | NM_000380.4 | c.683G>A | p.Arg228Gln | missense_variant | 6/6 | ENST00000375128.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XPA | ENST00000375128.5 | c.683G>A | p.Arg228Gln | missense_variant | 6/6 | 1 | NM_000380.4 | P1 | |
XPA | ENST00000485042.1 | n.195G>A | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
XPA | ENST00000462523.5 | c.*119G>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152000Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000211 AC: 53AN: 250986Hom.: 0 AF XY: 0.000229 AC XY: 31AN XY: 135636
GnomAD4 exome AF: 0.000174 AC: 254AN: 1461702Hom.: 1 Cov.: 31 AF XY: 0.000186 AC XY: 135AN XY: 727150
GnomAD4 genome ? AF: 0.000158 AC: 24AN: 152000Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74236
ClinVar
Submissions by phenotype
Xeroderma pigmentosum group A Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Nov 11, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 03, 2021 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Feb 07, 2017 | - - |
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden | Nov 03, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Oct 25, 2021 | - - |
Xeroderma pigmentosum Uncertain:1
Uncertain significance, criteria provided, single submitter | curation | Sema4, Sema4 | Feb 15, 2022 | - - |
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