rs33954001
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_000343.4(SLC5A1):āc.1845C>Gā(p.His615Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0655 in 1,613,006 control chromosomes in the GnomAD database, including 3,936 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 ). Synonymous variant affecting the same amino acid position (i.e. H615H) has been classified as Likely benign.
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 | UniProt |
---|---|---|---|---|---|---|---|
SLC5A1 | NM_000343.4 | c.1845C>G | p.His615Gln | missense_variant | 15/15 | ENST00000266088.9 | |
LOC105373000 | XR_938172.3 | n.408-3121G>C | intron_variant, non_coding_transcript_variant | ||||
SLC5A1 | NM_001256314.2 | c.1464C>G | p.His488Gln | missense_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC5A1 | ENST00000266088.9 | c.1845C>G | p.His615Gln | missense_variant | 15/15 | 1 | NM_000343.4 | P1 | |
SLC5A1 | ENST00000543737.2 | c.1464C>G | p.His488Gln | missense_variant | 14/14 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0450 AC: 6850AN: 152090Hom.: 207 Cov.: 32
GnomAD3 exomes AF: 0.0485 AC: 12189AN: 251408Hom.: 373 AF XY: 0.0495 AC XY: 6724AN XY: 135868
GnomAD4 exome AF: 0.0676 AC: 98770AN: 1460798Hom.: 3730 Cov.: 31 AF XY: 0.0668 AC XY: 48572AN XY: 726754
GnomAD4 genome ? AF: 0.0450 AC: 6851AN: 152208Hom.: 206 Cov.: 32 AF XY: 0.0435 AC XY: 3234AN XY: 74414
ClinVar
Submissions by phenotype
Congenital glucose-galactose malabsorption Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 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. - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | 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: MAF - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at