rs3803258

Positions:

• chr13-103044637-T-C

Variant summary

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

The NM_000452.3(SLC10A2):​c.*1496A>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 0.153 in 152,228 control chromosomes in the GnomAD database, including 2,018 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 0.15 (2017 hom., cov: 32)
  • Exomes 𝑓: 0.29 (1 hom.)
• Consequence: SLC10A2 NM_000452.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC10A2	NM_000452.3	c.*1496A>G		3_prime_UTR_variant	6/6	ENST00000245312.5	NP_000443.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC10A2	ENST00000245312	c.*1496A>G		3_prime_UTR_variant	6/6	1	NM_000452.3	ENSP00000245312.3

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23348 AN: 152096 Hom.: 2016 Cov.: 32

Gnomad AFR AF: 0.0810

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.144

GnomAD4 exome AF: 0.286 AC: 4 AN: 14 Hom.: 1 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.153 AC: 23357 AN: 152214 Hom.: 2017 Cov.: 32 AF XY: 0.156 AC XY: 11605 AN XY: 74430

Gnomad4 AFR AF: 0.0808

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.148

Alfa AF: 0.182 Hom.: 5561

Bravo AF: 0.143

Asia WGS AF: 0.223 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.54

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: rs3803258; hg19: chr13-103696987;