22-32043331-T-C
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_000343.4(SLC5A1):āc.50T>Cā(p.Val17Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00167 in 1,614,198 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_000343.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC5A1 | NM_000343.4 | c.50T>C | p.Val17Ala | missense_variant | 1/15 | ENST00000266088.9 | NP_000334.1 | |
SLC5A1 | XM_011530331.2 | c.50T>C | p.Val17Ala | missense_variant | 1/12 | XP_011528633.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC5A1 | ENST00000266088.9 | c.50T>C | p.Val17Ala | missense_variant | 1/15 | 1 | NM_000343.4 | ENSP00000266088 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00728 AC: 1108AN: 152220Hom.: 15 Cov.: 32
GnomAD3 exomes AF: 0.00242 AC: 606AN: 250766Hom.: 4 AF XY: 0.00183 AC XY: 248AN XY: 135634
GnomAD4 exome AF: 0.00108 AC: 1579AN: 1461860Hom.: 17 Cov.: 32 AF XY: 0.000994 AC XY: 723AN XY: 727228
GnomAD4 genome AF: 0.00729 AC: 1111AN: 152338Hom.: 15 Cov.: 32 AF XY: 0.00640 AC XY: 477AN XY: 74496
ClinVar
Submissions by phenotype
Congenital glucose-galactose malabsorption Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | 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. - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at