X-48905162-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_005660.3(SLC35A2):c.747G>A(p.Gly249Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000215 in 1,208,385 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005660.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000977 AC: 11AN: 112612Hom.: 0 Cov.: 23 AF XY: 0.0000576 AC XY: 2AN XY: 34744
GnomAD3 exomes AF: 0.0000457 AC: 8AN: 174947Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 61269
GnomAD4 exome AF: 0.0000137 AC: 15AN: 1095773Hom.: 0 Cov.: 31 AF XY: 0.00000553 AC XY: 2AN XY: 361429
GnomAD4 genome AF: 0.0000977 AC: 11AN: 112612Hom.: 0 Cov.: 23 AF XY: 0.0000576 AC XY: 2AN XY: 34744
ClinVar
Submissions by phenotype
Inborn genetic diseases 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. -
SLC35A2-congenital disorder of glycosylation Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at