rs1077858

chr11-75190556-G-A

Variant summary

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

The NM_007256.5(SLCO2B1):c.1075+2318G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,080 control chromosomes in the GnomAD database, including 28,889 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 0.61 (28889 hom., cov: 32)
• Consequence: SLCO2B1 NM_007256.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.12

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO2B1	NM_007256.5	c.1075+2318G>A		intron_variant		ENST00000289575.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO2B1	ENST00000289575.10	c.1075+2318G>A		intron_variant		1	NM_007256.5	P2

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93113 AN: 151958 Hom.: 28870 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.613 AC: 93176 AN: 152080 Hom.: 28889 Cov.: 32 AF XY: 0.612 AC XY: 45515 AN XY: 74324

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.616

Alfa AF: 0.644 Hom.: 36080

Bravo AF: 0.609

Asia WGS AF: 0.517 AC: 1800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.16
Dann	Benign	0.48

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: rs1077858; hg19: chr11-74901601;