2-216137192-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_021141.4(XRCC5):c.1218C>T(p.Gly406Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,613,360 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 Likely benign (★).
Frequency
Consequence
NM_021141.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XRCC5 | ENST00000392132.7 | c.1218C>T | p.Gly406Gly | synonymous_variant | Exon 11 of 21 | 1 | NM_021141.4 | ENSP00000375977.2 | ||
XRCC5 | ENST00000460284.5 | n.1760C>T | non_coding_transcript_exon_variant | Exon 8 of 18 | 1 | |||||
XRCC5 | ENST00000392133.7 | c.1218C>T | p.Gly406Gly | synonymous_variant | Exon 13 of 23 | 5 | ENSP00000375978.3 | |||
XRCC5 | ENST00000471649.1 | n.352C>T | non_coding_transcript_exon_variant | Exon 4 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250742Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135528
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461064Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 726790
GnomAD4 genome AF: 0.000131 AC: 20AN: 152296Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74482
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at