chr14-69778340-A-C
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_003049.4(SLC10A1):āc.936T>Gā(p.Thr312=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,603,232 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: š 0.000026 ( 0 hom., cov: 31)
Exomes š: 0.0000090 ( 0 hom. )
Consequence
SLC10A1
NM_003049.4 synonymous
NM_003049.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.303
Genes affected
SLC10A1 (HGNC:10905): (solute carrier family 10 member 1) The protein encoded by this gene belongs to the sodium/bile acid cotransporter family, which are integral membrane glycoproteins that participate in the enterohepatic circulation of bile acids. Two homologous transporters are involved in the reabsorption of bile acids; the ileal sodium/bile acid cotransporter with an apical cell localization that absorbs bile acids from the intestinal lumen, bile duct and kidney, and the liver-specific sodium/bile acid cotransporter, represented by this protein, that is found in the basolateral membranes of hepatocytes. Bile acids are the catabolic product of cholesterol metabolism, hence this protein is important for cholesterol homeostasis. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 14-69778340-A-C is Benign according to our data. Variant chr14-69778340-A-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 597939.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
BP7
Synonymous conserved (PhyloP=0.303 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC10A1 | NM_003049.4 | c.936T>G | p.Thr312= | synonymous_variant | 4/5 | ENST00000216540.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC10A1 | ENST00000216540.5 | c.936T>G | p.Thr312= | synonymous_variant | 4/5 | 1 | NM_003049.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152108Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000456 AC: 11AN: 241438Hom.: 0 AF XY: 0.0000154 AC XY: 2AN XY: 130212
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GnomAD4 exome AF: 0.00000896 AC: 13AN: 1451006Hom.: 0 Cov.: 30 AF XY: 0.00000554 AC XY: 4AN XY: 721416
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152226Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74440
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 05, 2018 | - - |
SLC10A1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 03, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at