rs1789693

Positions:

• chr11-75176120-T-A
• chr11-75176120-T-C

Variant summary

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

The NM_007256.5(SLCO2B1):​c.972+3551T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 152,084 control chromosomes in the GnomAD database, including 25,324 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 0.56 (25324 hom., cov: 32)
• Consequence: SLCO2B1 NM_007256.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217

Genes affected

SLCO2B1 (HGNC:10962): (solute carrier organic anion transporter family member 2B1) This locus encodes a member of the organic anion-transporting polypeptide family of membrane proteins. The protein encoded by this locus may function in regulation of placental uptake of sulfated steroids. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 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 = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO2B1	NM_007256.5	c.972+3551T>A		intron_variant		ENST00000289575.10	NP_009187.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO2B1	ENST00000289575.10	c.972+3551T>A		intron_variant		1	NM_007256.5	ENSP00000289575	P2

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84746 AN: 151966 Hom.: 25332 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.557 AC: 84764 AN: 152084 Hom.: 25324 Cov.: 32 AF XY: 0.564 AC XY: 41927 AN XY: 74356

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.586

Alfa AF: 0.472 Hom.: 1401

Bravo AF: 0.540

Asia WGS AF: 0.533 AC: 1857 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	3.1
DANN	Benign	0.85

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: rs1789693; hg19: chr11-74887165;