chr11-75175029-G-A

Variant names:

• chr11-75175029-G-A
• rs7947726
• NM_007256.5:c.972+2460G>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.972+2460G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,148 control chromosomes in the GnomAD database, including 1,735 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 0.14 (1735 hom., cov: 32)
• Consequence: SLCO2B1 NM_007256.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 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.972+2460G>A		intron	N/A	NP_009187.1
	SLCO2B1	NM_001145211.3		c.906+2460G>A		intron	N/A	NP_001138683.1
	SLCO2B1	NM_001145212.3		c.540+2460G>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.972+2460G>A		intron	N/A	ENSP00000289575.5
	SLCO2B1	ENST00000428359.6	TSL:1	c.906+2460G>A		intron	N/A	ENSP00000388912.2
	SLCO2B1	ENST00000532236.5	TSL:2	c.624+2460G>A		intron	N/A	ENSP00000434112.1

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21107 AN: 152030 Hom.: 1729 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.00539

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.139 AC: 21145 AN: 152148 Hom.: 1735 Cov.: 32 AF XY: 0.137 AC XY: 10169 AN XY: 74386

African (AFR) AF: 0.221 AC: 9168 AN: 41490

American (AMR) AF: 0.103 AC: 1576 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 755 AN: 3470

East Asian (EAS) AF: 0.00541 AC: 28 AN: 5180

South Asian (SAS) AF: 0.110 AC: 531 AN: 4820

European-Finnish (FIN) AF: 0.105 AC: 1108 AN: 10574

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7467 AN: 68000

Other (OTH) AF: 0.149 AC: 314 AN: 2112

Alfa AF: 0.121 Hom.: 1962

Bravo AF: 0.142

Asia WGS AF: 0.0930 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.68
PhyloP100		0.20
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: rs7947726; hg19: chr11-74886074;