Variant rs41281678 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The ENST00000245312.5(SLC10A2):c.505C>T(p.Leu169=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.024 in 1,596,202 control chromosomes in the GnomAD database, including 561 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.026 ( 76 hom., cov: 32)

Exomes 𝑓: 0.024 ( 485 hom. )

Consequence

SLC10A2
ENST00000245312.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.31

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 13-103052700-G-A is Benign according to our data. Variant chr13-103052700-G-A is described in ClinVar as [Benign]. Clinvar id is 501366.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.31 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0263 (4001/152240) while in subpopulation AFR AF= 0.0401 (1664/41540). AF 95% confidence interval is 0.0385. There are 76 homozygotes in gnomad4. There are 1894 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 4001 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC10A2	NM_000452.3 linkuse as main transcript	c.505C>T	p.Leu169=	synonymous_variant	3/6	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.505C>T	p.Leu169=	synonymous_variant	3/6	1	NM_000452.3	ENSP00000245312	P1

Frequencies

GnomAD3 genomes

AF:

0.0262

AC:

3990

AN:

152122

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0398

Gnomad AMI

AF:

0.0537

Gnomad AMR

AF:

0.0209

Gnomad ASJ

AF:

0.0173

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0195

Gnomad FIN

AF:

0.0104

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0244

Gnomad OTH

AF:

0.0196

GnomAD3 exomes

AF:

0.0194

AC:

4862

AN:

251120

Hom.:

AF XY:

0.0196

AC XY:

2655

AN XY:

135718

show subpopulations

Gnomad AFR exome

AF:

0.0381

Gnomad AMR exome

AF:

0.0111

Gnomad ASJ exome

AF:

0.0169

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0231

Gnomad FIN exome

AF:

0.00883

Gnomad NFE exome

AF:

0.0235

Gnomad OTH exome

AF:

0.0203

GnomAD4 exome

AF:

0.0238

AC:

34302

AN:

1443962

Hom.:

485

Cov.:

AF XY:

0.0237

AC XY:

17087

AN XY:

719578

show subpopulations

Gnomad4 AFR exome

AF:

0.0426

Gnomad4 AMR exome

AF:

0.0113

Gnomad4 ASJ exome

AF:

0.0176

Gnomad4 EAS exome

AF:

0.0000505

Gnomad4 SAS exome

AF:

0.0238

Gnomad4 FIN exome

AF:

0.00967

Gnomad4 NFE exome

AF:

0.0254

Gnomad4 OTH exome

AF:

0.0234

GnomAD4 genome

AF:

0.0263

AC:

4001

AN:

152240

Hom.:

Cov.:

AF XY:

0.0254

AC XY:

1894

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0401

Gnomad4 AMR

AF:

0.0208

Gnomad4 ASJ

AF:

0.0173

Gnomad4 EAS

AF:

0.000772

Gnomad4 SAS

AF:

0.0193

Gnomad4 FIN

AF:

0.0104

Gnomad4 NFE

AF:

0.0244

Gnomad4 OTH

AF:

0.0194

Alfa

AF:

0.0241

Hom.:

Bravo

AF:

0.0275

Asia WGS

AF:

0.00808

AC:

AN:

3478

EpiCase

AF:

0.0261

EpiControl

AF:

0.0254

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

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

Apr 11, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

1.5

DANN

Benign

0.42

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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