rs1060503676
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_005660.3(SLC35A2):c.535G>A(p.Val179Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000111 in 1,080,266 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005660.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome AF: 0.0000111 AC: 12AN: 1080266Hom.: 0 Cov.: 31 AF XY: 0.0000114 AC XY: 4AN XY: 351728
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
SLC35A2-congenital disorder of glycosylation Uncertain:1
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. This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 179 of the SLC35A2 protein (p.Val179Ile). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SLC35A2-related conditions. ClinVar contains an entry for this variant (Variation ID: 412237). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at