14-103699416-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005432.4(XRCC3):c.722C>T(p.Thr241Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 1,611,814 control chromosomes in the GnomAD database, including 98,522 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005432.4 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 |
---|---|---|---|---|---|---|---|
XRCC3 | NM_005432.4 | c.722C>T | p.Thr241Met | missense_variant | 8/10 | ENST00000555055.6 | |
KLC1 | NM_001394837.1 | c.1849-1239G>A | intron_variant | ENST00000334553.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XRCC3 | ENST00000555055.6 | c.722C>T | p.Thr241Met | missense_variant | 8/10 | 1 | NM_005432.4 | P1 | |
KLC1 | ENST00000334553.11 | c.1849-1239G>A | intron_variant | 5 | NM_001394837.1 |
Frequencies
GnomAD3 genomes AF: 0.298 AC: 45211AN: 151816Hom.: 7375 Cov.: 32
GnomAD3 exomes AF: 0.290 AC: 71621AN: 246952Hom.: 11812 AF XY: 0.298 AC XY: 40018AN XY: 134296
GnomAD4 exome AF: 0.346 AC: 504514AN: 1459878Hom.: 91144 Cov.: 56 AF XY: 0.345 AC XY: 250452AN XY: 726268
GnomAD4 genome AF: 0.298 AC: 45218AN: 151936Hom.: 7378 Cov.: 32 AF XY: 0.291 AC XY: 21629AN XY: 74296
ClinVar
Submissions by phenotype
XRCC3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 08, 2023 | - - |
Melanoma, cutaneous malignant, susceptibility to, 6 Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Oct 15, 2000 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at