Variant 13-103046280-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000245312.5(SLC10A2):c.920-20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 1,593,310 control chromosomes in the GnomAD database, including 608,254 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.88 ( 59115 hom., cov: 32)

Exomes 𝑓: 0.87 ( 549139 hom. )

Consequence

SLC10A2
ENST00000245312.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.0910

Variant links:

Genes affected

SLC10A2 (HGNC:10906): (solute carrier family 10 member 2) This gene encodes a sodium/bile acid cotransporter. This transporter is the primary mechanism for uptake of intestinal bile acids by apical cells in the distal ileum. Bile acids are the catabolic product of cholesterol metabolism, so this protein is also critical for cholesterol homeostasis. Mutations in this gene cause primary bile acid malabsorption (PBAM); muatations in this gene may also be associated with other diseases of the liver and intestines, such as familial hypertriglyceridemia (FHTG). [provided by RefSeq, Mar 2010]

SLC10A2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 13-103046280-C-T is Benign according to our data. Variant chr13-103046280-C-T is described in ClinVar as [Benign]. Clinvar id is 1332970.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-103046280-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC10A2	NM_000452.3 linkuse as main transcript	c.920-20G>A		intron_variant		ENST00000245312.5	NP_000443.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC10A2	ENST00000245312.5 linkuse as main transcript	c.920-20G>A		intron_variant		1	NM_000452.3	ENSP00000245312	P1

Frequencies

GnomAD3 genomes

AF:

0.880

AC:

133868

AN:

152120

Hom.:

59067

Cov.:

show subpopulations

Gnomad AFR

AF:

0.926

Gnomad AMI

AF:

0.975

Gnomad AMR

AF:

0.808

Gnomad ASJ

AF:

0.868

Gnomad EAS

AF:

0.740

Gnomad SAS

AF:

0.849

Gnomad FIN

AF:

0.880

Gnomad MID

AF:

0.839

Gnomad NFE

AF:

0.881

Gnomad OTH

AF:

0.868

GnomAD3 exomes

AF:

0.855

AC:

208955

AN:

244460

Hom.:

89772

AF XY:

0.858

AC XY:

113580

AN XY:

132310

show subpopulations

Gnomad AFR exome

AF:

0.926

Gnomad AMR exome

AF:

0.760

Gnomad ASJ exome

AF:

0.873

Gnomad EAS exome

AF:

0.737

Gnomad SAS exome

AF:

0.866

Gnomad FIN exome

AF:

0.883

Gnomad NFE exome

AF:

0.882

Gnomad OTH exome

AF:

0.864

GnomAD4 exome

AF:

0.872

AC:

1256485

AN:

1441072

Hom.:

549139

Cov.:

AF XY:

0.872

AC XY:

626012

AN XY:

718048

show subpopulations

Gnomad4 AFR exome

AF:

0.928

Gnomad4 AMR exome

AF:

0.765

Gnomad4 ASJ exome

AF:

0.871

Gnomad4 EAS exome

AF:

0.728

Gnomad4 SAS exome

AF:

0.865

Gnomad4 FIN exome

AF:

0.886

Gnomad4 NFE exome

AF:

0.880

Gnomad4 OTH exome

AF:

0.868

GnomAD4 genome

AF:

0.880

AC:

133969

AN:

152238

Hom.:

59115

Cov.:

AF XY:

0.877

AC XY:

65251

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.926

Gnomad4 AMR

AF:

0.808

Gnomad4 ASJ

AF:

0.868

Gnomad4 EAS

AF:

0.739

Gnomad4 SAS

AF:

0.849

Gnomad4 FIN

AF:

0.880

Gnomad4 NFE

AF:

0.881

Gnomad4 OTH

AF:

0.870

Alfa

AF:

0.877

Hom.:

61917

Bravo

AF:

0.876

Asia WGS

AF:

0.813

AC:

2829

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

Bile acid malabsorption, primary, 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.2

DANN

Benign

0.17

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over