rs25487
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_StrongBA1
The NM_006297.3(XRCC1):c.1196A>G(p.Gln399Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 1,613,104 control chromosomes in the GnomAD database, including 351,454 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as drug response (★★★).
Frequency
Consequence
NM_006297.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XRCC1 | NM_006297.3 | c.1196A>G | p.Gln399Arg | missense_variant | 10/17 | ENST00000262887.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XRCC1 | ENST00000262887.10 | c.1196A>G | p.Gln399Arg | missense_variant | 10/17 | 1 | NM_006297.3 | P1 | |
XRCC1 | ENST00000543982.5 | c.1103A>G | p.Gln368Arg | missense_variant | 9/16 | 2 | |||
XRCC1 | ENST00000597811.5 | c.*310A>G | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.711 AC: 108110AN: 152018Hom.: 39012 Cov.: 33
GnomAD3 exomes AF: 0.681 AC: 170473AN: 250468Hom.: 58636 AF XY: 0.673 AC XY: 91132AN XY: 135456
GnomAD4 exome AF: 0.652 AC: 952451AN: 1460968Hom.: 312387 Cov.: 39 AF XY: 0.652 AC XY: 473566AN XY: 726870
GnomAD4 genome AF: 0.711 AC: 108216AN: 152136Hom.: 39067 Cov.: 33 AF XY: 0.713 AC XY: 53053AN XY: 74358
ClinVar
Submissions by phenotype
Spinocerebellar ataxia, autosomal recessive 26 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 31, 2020 | This variant is associated with the following publications: (PMID: 21427728, 15113441, 19481337, 11782372, 23479765, 14630517, 21843798, 22053659, 22951806, 24176953, 22224629, 22106831, 23360319, 21987112, 21928248, 18641418, 22193858, 19012493, 22525558, 22712837, 19880550, 22302399, 22983827, 21617750, 20431719, 23499241, 19465687, 20385586, 18357393, 21647176, 19051060, 23055018, 17961713, 22868082, 22568010, 19428062, 11104903, 24205020) - |
Platinum compounds response - Efficacy Other:1
drug response, reviewed by expert panel | curation | PharmGKB | Mar 24, 2021 | PharmGKB Level of Evidence 2B: Variants in Level 2B clinical annotations are not in PharmGKB’s Tier 1 VIPs. These clinical annotations describe variant-drug combinations with a moderate level of evidence supporting the association. For example, the association may be found in multiple cohorts, but there may be a minority of studies that do not support the majority assertion. Level 2B clinical annotations must be supported by at least two independent publications. Drug-variant association: Efficacy |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at