chr13-103062967-A-C

Position:

• chr13-103062967-A-C

Variant summary

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

The ENST00000245312.5(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 ENST00000245312.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131

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=-0.91).
• 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/exons	MANE	Protein	UniProt
SLC10A2	NM_000452.3	c.377+2906T>G		intron_variant		ENST00000245312.5	NP_000443.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC10A2	ENST00000245312.5	c.377+2906T>G		intron_variant		1	NM_000452.3	ENSP00000245312	P1

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

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.846

Gnomad4 ASJ AF: 0.873

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.908

Gnomad4 OTH AF: 0.870

Alfa AF: 0.893 Hom.: 21001

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

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: rs1886927; hg19: chr13-103715317;