Variant chr13-103066121-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_000452.3(SLC10A2):c.129C>T(p.Ala43=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0197 in 1,614,020 control chromosomes in the GnomAD database, including 402 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.024 ( 64 hom., cov: 32)

Exomes 𝑓: 0.019 ( 338 hom. )

Consequence

SLC10A2
NM_000452.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.193

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 13-103066121-G-A is Benign according to our data. Variant chr13-103066121-G-A is described in ClinVar as [Benign]. Clinvar id is 2122470.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.193 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0242 (3690/152230) while in subpopulation AFR AF= 0.0361 (1500/41546). AF 95% confidence interval is 0.0346. There are 64 homozygotes in gnomad4. There are 1712 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 3690 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC10A2	NM_000452.3 linkuse as main transcript	c.129C>T	p.Ala43=	synonymous_variant	1/6	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.129C>T	p.Ala43=	synonymous_variant	1/6	1	NM_000452.3	ENSP00000245312	P1

Frequencies

GnomAD3 genomes

AF:

0.0243

AC:

3691

AN:

152110

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0362

Gnomad AMI

AF:

0.0526

Gnomad AMR

AF:

0.0128

Gnomad ASJ

AF:

0.0730

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00455

Gnomad FIN

AF:

0.0121

Gnomad MID

AF:

0.0548

Gnomad NFE

AF:

0.0217

Gnomad OTH

AF:

0.0240

GnomAD3 exomes

AF:

0.0185

AC:

4649

AN:

251448

Hom.:

AF XY:

0.0178

AC XY:

2420

AN XY:

135892

show subpopulations

Gnomad AFR exome

AF:

0.0378

Gnomad AMR exome

AF:

0.00824

Gnomad ASJ exome

AF:

0.0640

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.00719

Gnomad FIN exome

AF:

0.0122

Gnomad NFE exome

AF:

0.0218

Gnomad OTH exome

AF:

0.0222

GnomAD4 exome

AF:

0.0192

AC:

28125

AN:

1461790

Hom.:

338

Cov.:

AF XY:

0.0191

AC XY:

13914

AN XY:

727200

show subpopulations

Gnomad4 AFR exome

AF:

0.0388

Gnomad4 AMR exome

AF:

0.00861

Gnomad4 ASJ exome

AF:

0.0644

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00669

Gnomad4 FIN exome

AF:

0.0118

Gnomad4 NFE exome

AF:

0.0198

Gnomad4 OTH exome

AF:

0.0213

GnomAD4 genome

AF:

0.0242

AC:

3690

AN:

152230

Hom.:

Cov.:

AF XY:

0.0230

AC XY:

1712

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.0361

Gnomad4 AMR

AF:

0.0128

Gnomad4 ASJ

AF:

0.0730

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00455

Gnomad4 FIN

AF:

0.0121

Gnomad4 NFE

AF:

0.0217

Gnomad4 OTH

AF:

0.0237

Alfa

AF:

0.0249

Hom.:

Bravo

AF:

0.0246

Asia WGS

AF:

0.0110

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

5.0

DANN

Benign

0.59

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