22-32043314-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000343.4(SLC5A1):c.33C>T(p.Thr11=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,614,062 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
SLC5A1
NM_000343.4 synonymous
NM_000343.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.83
Genes affected
SLC5A1 (HGNC:11036): (solute carrier family 5 member 1) This gene encodes a member of the sodium-dependent glucose transporter (SGLT) family. The encoded integral membrane protein is the primary mediator of dietary glucose and galactose uptake from the intestinal lumen. Mutations in this gene have been associated with glucose-galactose malabsorption. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 22-32043314-C-T is Benign according to our data. Variant chr22-32043314-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2887028.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.83 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC5A1 | NM_000343.4 | c.33C>T | p.Thr11= | synonymous_variant | 1/15 | ENST00000266088.9 | NP_000334.1 | |
SLC5A1 | XM_011530331.2 | c.33C>T | p.Thr11= | synonymous_variant | 1/12 | XP_011528633.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC5A1 | ENST00000266088.9 | c.33C>T | p.Thr11= | synonymous_variant | 1/15 | 1 | NM_000343.4 | ENSP00000266088 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152240Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250764Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135636
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GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461822Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 727218
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74374
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital glucose-galactose malabsorption Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 08, 2023 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at