rs279941

chr13-103045818-A-Cchr13-103045818-A-Gchr13-103045818-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000452.3(SLC10A2):c.*315T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 210,524 control chromosomes in the GnomAD database, including 81,136 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.88 (59000 hom., cov: 29)
  • Exomes 𝑓: 0.87 (22136 hom.)
• Consequence: SLC10A2 NM_000452.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• 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	UniProt
SLC10A2	NM_000452.3	c.*315T>G		3_prime_UTR_variant	6/6	ENST00000245312.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC10A2	ENST00000245312.5	c.*315T>G		3_prime_UTR_variant	6/6	1	NM_000452.3	P1

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133587 AN: 151788 Hom.: 58949 Cov.: 29

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.841

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.867

GnomAD4 exome AF: 0.866 AC: 50782 AN: 58618 Hom.: 22136 Cov.: 2 AF XY: 0.866 AC XY: 26943 AN XY: 31106

Gnomad4 AFR exome AF: 0.921

Gnomad4 AMR exome AF: 0.781

Gnomad4 ASJ exome AF: 0.866

Gnomad4 EAS exome AF: 0.734

Gnomad4 SAS exome AF: 0.858

Gnomad4 FIN exome AF: 0.883

Gnomad4 NFE exome AF: 0.883

Gnomad4 OTH exome AF: 0.889

GnomAD4 genome AF: 0.880 AC: 133691 AN: 151906 Hom.: 59000 Cov.: 29 AF XY: 0.877 AC XY: 65104 AN XY: 74232

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.808

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.880

Gnomad4 NFE AF: 0.881

Gnomad4 OTH AF: 0.869

Alfa AF: 0.877 Hom.: 113384

Bravo AF: 0.876

Asia WGS AF: 0.815 AC: 2824 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.045
Dann	Benign	0.48

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

Other links and lift over

dbSNP: rs279941; hg19: chr13-103698168;