19-43560950-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006297.3(XRCC1):āc.215T>Cā(p.Val72Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0032 in 1,614,150 control chromosomes in the GnomAD database, including 139 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_006297.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XRCC1 | NM_006297.3 | c.215T>C | p.Val72Ala | missense_variant | 3/17 | ENST00000262887.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XRCC1 | ENST00000262887.10 | c.215T>C | p.Val72Ala | missense_variant | 3/17 | 1 | NM_006297.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0172 AC: 2624AN: 152148Hom.: 73 Cov.: 32
GnomAD3 exomes AF: 0.00433 AC: 1089AN: 251472Hom.: 22 AF XY: 0.00319 AC XY: 433AN XY: 135910
GnomAD4 exome AF: 0.00173 AC: 2531AN: 1461884Hom.: 65 Cov.: 31 AF XY: 0.00153 AC XY: 1111AN XY: 727248
GnomAD4 genome AF: 0.0173 AC: 2637AN: 152266Hom.: 74 Cov.: 32 AF XY: 0.0167 AC XY: 1242AN XY: 74450
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
XRCC1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 14, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at