chr13-103049423-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_000452.3(SLC10A2):c.785C>T(p.Thr262Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000496 in 1,613,904 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T262K) has been classified as Uncertain significance.
Frequency
Consequence
NM_000452.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC10A2 | NM_000452.3 | c.785C>T | p.Thr262Met | missense_variant | 5/6 | ENST00000245312.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC10A2 | ENST00000245312.5 | c.785C>T | p.Thr262Met | missense_variant | 5/6 | 1 | NM_000452.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000513 AC: 78AN: 152082Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000529 AC: 133AN: 251356Hom.: 0 AF XY: 0.000567 AC XY: 77AN XY: 135842
GnomAD4 exome AF: 0.000494 AC: 722AN: 1461704Hom.: 0 Cov.: 31 AF XY: 0.000503 AC XY: 366AN XY: 727154
GnomAD4 genome AF: 0.000512 AC: 78AN: 152200Hom.: 1 Cov.: 32 AF XY: 0.000605 AC XY: 45AN XY: 74420
ClinVar
Submissions by phenotype
not provided Uncertain:3Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 09, 2023 | PP3, PS3 - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 07, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 23, 2018 | - - |
Bile acid malabsorption, primary, 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Mar 14, 2024 | - - |
SLC10A2-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 14, 2023 | The SLC10A2 c.785C>T variant is predicted to result in the amino acid substitution p.Thr262Met. This variant was reported in a single individual with autosomal recessive primary bile acid malabsorption, but it was detected in cis (on the same chromosome) with a more rare variant (Oelkers et al. 1997. PubMed ID: 9109432). Functional studies have supported the pathogenicity of both changes alone, and as a complex allele, thus not allowing definitive conclusions about which may be causative (Ho et al. 2011. PubMed ID: 21649730). In ClinVar this alteration is interpreted as a variant of uncertain significance (https://www.ncbi.nlm.nih.gov/clinvar/variation/242727/evidence/). Although it's possible that this variant could be pathogenic, its clinical significance remains uncertain at this time due to insufficient functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at