rs157266

Variant names:

• chr13-103060149-A-G
• rs157266
• NM_000452.3:c.378-1767T>C

Your query was ambiguous. Multiple possible variants found:

• chr13-103060149-A-G
• chr13-103060149-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.378-1767T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,128 control chromosomes in the GnomAD database, including 58,915 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 (58915 hom., cov: 30)
• Consequence: SLC10A2 NM_000452.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC10A2	NM_000452.3	c.378-1767T>C		intron_variant	Intron 1 of 5	ENST00000245312.5	NP_000443.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC10A2	ENST00000245312.5	c.378-1767T>C		intron_variant	Intron 1 of 5	1	NM_000452.3	ENSP00000245312.3

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133737 AN: 152010 Hom.: 58871 Cov.: 30

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.870

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.880 AC: 133833 AN: 152128 Hom.: 58915 Cov.: 30 AF XY: 0.878 AC XY: 65255 AN XY: 74364

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.850

Gnomad4 FIN AF: 0.878

Gnomad4 NFE AF: 0.883

Gnomad4 OTH AF: 0.872

Alfa AF: 0.882 Hom.: 80717

Bravo AF: 0.878

Asia WGS AF: 0.838 AC: 2915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.98
DANN	Benign	0.38

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: rs157266; hg19: chr13-103712499;