chr14-103699410-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005432.4(XRCC3):c.728G>A(p.Arg243His) variant causes a missense change. The variant allele was found at a frequency of 0.00109 in 1,612,440 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R243C) has been classified as Uncertain significance.
Frequency
Consequence
NM_005432.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XRCC3 | NM_005432.4 | c.728G>A | p.Arg243His | missense_variant | 8/10 | ENST00000555055.6 | |
KLC1 | NM_001394837.1 | c.1849-1245C>T | intron_variant | ENST00000334553.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XRCC3 | ENST00000555055.6 | c.728G>A | p.Arg243His | missense_variant | 8/10 | 1 | NM_005432.4 | P1 | |
KLC1 | ENST00000334553.11 | c.1849-1245C>T | intron_variant | 5 | NM_001394837.1 |
Frequencies
GnomAD3 genomes AF: 0.00558 AC: 849AN: 152180Hom.: 12 Cov.: 33
GnomAD3 exomes AF: 0.00147 AC: 363AN: 246918Hom.: 2 AF XY: 0.00108 AC XY: 145AN XY: 134334
GnomAD4 exome AF: 0.000623 AC: 909AN: 1460142Hom.: 7 Cov.: 31 AF XY: 0.000541 AC XY: 393AN XY: 726384
GnomAD4 genome AF: 0.00557 AC: 849AN: 152298Hom.: 12 Cov.: 33 AF XY: 0.00547 AC XY: 407AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at