rs2712800

Variant names:

• chr11-75141055-T-G
• rs2712800
• ENST00000531713.5:c.-50-21600T>G

Variant summary

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

The ENST00000531713.5(SLCO2B1):​c.-50-21600T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,104 control chromosomes in the GnomAD database, including 20,701 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 0.51 (20701 hom., cov: 32)
• Consequence: SLCO2B1 ENST00000531713.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO2B1	ENST00000531713.5	c.-50-21600T>G		intron_variant	Intron 1 of 3	3		ENSP00000432889.1
SLCO2B1	ENST00000526660.5	n.294-31324T>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76926 AN: 151986 Hom.: 20697 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.506 AC: 76966 AN: 152104 Hom.: 20701 Cov.: 32 AF XY: 0.505 AC XY: 37539 AN XY: 74360

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.550

Alfa AF: 0.569 Hom.: 11883

Bravo AF: 0.488

Asia WGS AF: 0.370 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2712800; hg19: chr11-74852100;