rs5406
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000340.2(SLC2A2):c.776-15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,605,918 control chromosomes in the GnomAD database, including 19,290 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000340.2 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: 0.208 AC: 31505AN: 151808Hom.: 4442 Cov.: 32
GnomAD3 exomes AF: 0.142 AC: 35469AN: 249130Hom.: 3350 AF XY: 0.141 AC XY: 19045AN XY: 134720
GnomAD4 exome AF: 0.133 AC: 192893AN: 1453992Hom.: 14838 Cov.: 30 AF XY: 0.133 AC XY: 96359AN XY: 723812
GnomAD4 genome AF: 0.208 AC: 31544AN: 151926Hom.: 4452 Cov.: 32 AF XY: 0.206 AC XY: 15286AN XY: 74264
ClinVar
Submissions by phenotype
not specified Benign:2
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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. -
Fanconi-Bickel syndrome Benign:2
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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not provided Benign:2
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Type 2 diabetes mellitus Benign:1
SLC2A2-rs5406 plays a role in occurence of T2DM. Its associated with neonatal diabetes, glycogen accumulation in liver leading to hepatomegaly. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at