21-39390723-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004627.6(GET1):c.128C>T(p.Ala43Val) variant causes a missense change. The variant allele was found at a frequency of 0.000018 in 1,613,952 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004627.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GET1 | ENST00000649170.1 | c.128C>T | p.Ala43Val | missense_variant | Exon 2 of 5 | NM_004627.6 | ENSP00000496813.1 | |||
GET1-SH3BGR | ENST00000647779.1 | c.128C>T | p.Ala43Val | missense_variant | Exon 2 of 9 | ENSP00000497977.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251368Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135876
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461872Hom.: 0 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 727236
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74262
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.128C>T (p.A43V) alteration is located in exon 2 (coding exon 2) of the WRB gene. This alteration results from a C to T substitution at nucleotide position 128, causing the alanine (A) at amino acid position 43 to be replaced by a valine (V). 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