14-103698901-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_005432.4(XRCC3):c.938G>A(p.Arg313Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00002 in 1,602,348 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005432.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XRCC3 | ENST00000555055.6 | c.938G>A | p.Arg313Gln | missense_variant | Exon 10 of 10 | 1 | NM_005432.4 | ENSP00000452598.1 | ||
KLC1 | ENST00000334553.11 | c.1849-1754C>T | intron_variant | Intron 15 of 16 | 5 | NM_001394837.1 | ENSP00000334523.6 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152134Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000268 AC: 6AN: 224202Hom.: 0 AF XY: 0.0000164 AC XY: 2AN XY: 122242
GnomAD4 exome AF: 0.0000186 AC: 27AN: 1450096Hom.: 0 Cov.: 32 AF XY: 0.0000194 AC XY: 14AN XY: 720292
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152252Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74428
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.938G>A (p.R313Q) alteration is located in exon 10 (coding exon 7) of the XRCC3 gene. This alteration results from a G to A substitution at nucleotide position 938, causing the arginine (R) at amino acid position 313 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at