2-216141258-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_021141.4(XRCC5):c.1415C>T(p.Thr472Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,461,812 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T472S) has been classified as Uncertain significance.
Frequency
Consequence
NM_021141.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XRCC5 | ENST00000392132.7 | c.1415C>T | p.Thr472Ile | missense_variant | Exon 13 of 21 | 1 | NM_021141.4 | ENSP00000375977.2 | ||
XRCC5 | ENST00000460284.5 | n.1957C>T | non_coding_transcript_exon_variant | Exon 10 of 18 | 1 | |||||
XRCC5 | ENST00000392133.7 | c.1415C>T | p.Thr472Ile | missense_variant | Exon 15 of 23 | 5 | ENSP00000375978.3 | |||
XRCC5 | ENST00000471649.1 | n.549C>T | non_coding_transcript_exon_variant | Exon 6 of 6 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461812Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727210
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.