rs1886927

Variant names:

• chr13-103062967-A-C
• rs1886927
• NM_000452.3:c.377+2906T>G

Your query was ambiguous. Multiple possible variants found:

• chr13-103062967-A-C
• chr13-103062967-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000452.3(SLC10A2):​c.377+2906T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,046 control chromosomes in the GnomAD database, including 58,428 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 (58428 hom., cov: 30)
• Consequence: SLC10A2 NM_000452.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• bile acid malabsorption, primary, 1

  Inheritance: AR, Unknown Classification: LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), PanelApp Australia

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC10A2	NM_000452.3	c.377+2906T>G		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.377+2906T>G		intron_variant	Intron 1 of 5	1	NM_000452.3	ENSP00000245312.3

Frequencies

GnomAD3 genomes AF: 0.876 AC: 133022 AN: 151928 Hom.: 58389 Cov.: 30

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.875 AC: 133112 AN: 152046 Hom.: 58428 Cov.: 30 AF XY: 0.874 AC XY: 64968 AN XY: 74322

African (AFR) AF: 0.831 AC: 34475 AN: 41472

American (AMR) AF: 0.846 AC: 12926 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.873 AC: 3026 AN: 3468

East Asian (EAS) AF: 0.817 AC: 4206 AN: 5148

South Asian (SAS) AF: 0.872 AC: 4194 AN: 4808

European-Finnish (FIN) AF: 0.908 AC: 9596 AN: 10570

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.908 AC: 61706 AN: 67990

Other (OTH) AF: 0.870 AC: 1837 AN: 2112

Alfa AF: 0.884 Hom.: 30796

Bravo AF: 0.867

Asia WGS AF: 0.835 AC: 2905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.77
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1886927; hg19: chr13-103715317;