chr11-75155062-G-A

Variant names:

• chr11-75155062-G-A
• rs2712819
• NM_007256.5:c.16+3665G>A

Variant summary

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

The NM_007256.5(SLCO2B1):​c.16+3665G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.788 in 152,060 control chromosomes in the GnomAD database, including 47,471 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 0.79 (47471 hom., cov: 30)
• Consequence: SLCO2B1 NM_007256.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.08
• Publications: 8 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007256.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO2B1	NM_007256.5	MANE Select	c.16+3665G>A		intron	N/A	NP_009187.1
	SLCO2B1	NM_001145212.3		c.16+3665G>A		intron	N/A	NP_001138684.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO2B1	ENST00000289575.10	TSL:1 MANE Select	c.16+3665G>A		intron	N/A	ENSP00000289575.5
	SLCO2B1	ENST00000530556.5	TSL:1	c.-51+3232G>A		intron	N/A	ENSP00000435384.1
	SLCO2B1	ENST00000534004.5	TSL:1	c.-51+2546G>A		intron	N/A	ENSP00000431192.1

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119698 AN: 151942 Hom.: 47435 Cov.: 30

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.893

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.788 AC: 119788 AN: 152060 Hom.: 47471 Cov.: 30 AF XY: 0.793 AC XY: 58937 AN XY: 74338

African (AFR) AF: 0.692 AC: 28688 AN: 41434

American (AMR) AF: 0.837 AC: 12802 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3078 AN: 3468

East Asian (EAS) AF: 0.624 AC: 3216 AN: 5150

South Asian (SAS) AF: 0.894 AC: 4307 AN: 4820

European-Finnish (FIN) AF: 0.864 AC: 9152 AN: 10594

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55703 AN: 67986

Other (OTH) AF: 0.826 AC: 1743 AN: 2110

Alfa AF: 0.808 Hom.: 193537

Bravo AF: 0.780

Asia WGS AF: 0.795 AC: 2765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	19
DANN	Benign	0.79
PhyloP100		2.1
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: rs2712819; hg19: chr11-74866107;