rs2307191
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_006297.3(XRCC1):c.482C>T(p.Pro161Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000845 in 1,595,824 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Synonymous variant affecting the same amino acid position (i.e. P161P) has been classified as Likely benign.
Frequency
Consequence
NM_006297.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XRCC1 | NM_006297.3 | c.482C>T | p.Pro161Leu | missense_variant | 5/17 | ENST00000262887.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XRCC1 | ENST00000262887.10 | c.482C>T | p.Pro161Leu | missense_variant | 5/17 | 1 | NM_006297.3 | P1 | |
ENST00000597119.1 | n.83+89G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00452 AC: 686AN: 151764Hom.: 3 Cov.: 31
GnomAD3 exomes AF: 0.00125 AC: 306AN: 245186Hom.: 2 AF XY: 0.000839 AC XY: 111AN XY: 132304
GnomAD4 exome AF: 0.000456 AC: 658AN: 1443942Hom.: 5 Cov.: 33 AF XY: 0.000386 AC XY: 276AN XY: 715004
GnomAD4 genome ? AF: 0.00455 AC: 691AN: 151882Hom.: 3 Cov.: 31 AF XY: 0.00401 AC XY: 298AN XY: 74234
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at