rs56136150
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006416.5(SLC35A1):c.887-14T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0995 in 1,612,446 control chromosomes in the GnomAD database, including 8,338 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006416.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.108 AC: 16347AN: 152030Hom.: 923 Cov.: 32
GnomAD3 exomes AF: 0.106 AC: 26629AN: 251038Hom.: 1489 AF XY: 0.105 AC XY: 14225AN XY: 135740
GnomAD4 exome AF: 0.0987 AC: 144101AN: 1460298Hom.: 7414 Cov.: 33 AF XY: 0.0984 AC XY: 71462AN XY: 726540
GnomAD4 genome AF: 0.108 AC: 16366AN: 152148Hom.: 924 Cov.: 32 AF XY: 0.107 AC XY: 7989AN XY: 74388
ClinVar
Submissions by phenotype
not specified Benign:3
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
SLC35A1-congenital disorder of glycosylation Benign:1
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Congenital disorder of glycosylation Benign:1
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not provided Benign:1
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Pontoneocerebellar hypoplasia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at