X-2843067-C-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_003918.3(GYG2):c.77C>A(p.Ala26Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000166 in 541,734 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 53 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003918.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000894 AC: 10AN: 111824Hom.: 0 Cov.: 22 AF XY: 0.000118 AC XY: 4AN XY: 34014
GnomAD3 exomes AF: 0.000213 AC: 24AN: 112653Hom.: 0 AF XY: 0.000434 AC XY: 16AN XY: 36887
GnomAD4 exome AF: 0.000186 AC: 80AN: 429860Hom.: 0 Cov.: 6 AF XY: 0.000324 AC XY: 49AN XY: 151448
GnomAD4 genome AF: 0.0000894 AC: 10AN: 111874Hom.: 0 Cov.: 22 AF XY: 0.000117 AC XY: 4AN XY: 34074
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
This sequence change replaces alanine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 26 of the GYG2 protein (p.Ala26Asp). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with GYG2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1317898). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at