rs2712800

chr11-75141055-T-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO2B1	ENST00000531713.5	c.-50-21600T>G		intron_variant		3
SLCO2B1	ENST00000526660.5	n.294-31324T>G		intron_variant, non_coding_transcript_variant		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;