11-75131152-C-T

Position:

• chr11-75131152-C-T

Variant summary

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

The ENST00000531713.5(SLCO2B1):​c.-51+30297C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,850 control chromosomes in the GnomAD database, including 19,670 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 0.47 (19670 hom., cov: 31)
  • Exomes 𝑓: 0.59 (52252 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLCO2B1 ENST00000531713.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.846

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]

OR2AT1P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR2AT1P		n.75131152C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO2B1	ENST00000531713.5	c.-51+30297C>T		intron_variant		3		ENSP00000432889.1
OR2AT1P	ENST00000525935.1	n.729G>A		non_coding_transcript_exon_variant	1/1	6
SLCO2B1	ENST00000526660.5	n.293+30297C>T		intron_variant		3
ENSG00000255395	ENST00000530550.1	n.175+2667G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70897 AN: 151732 Hom.: 19677 Cov.: 31

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.527

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.587 AC: 169699 AN: 289330 Hom.: 52252 Cov.: 0 AF XY: 0.594 AC XY: 89407 AN XY: 150606

Gnomad4 AFR exome AF: 0.179

Gnomad4 AMR exome AF: 0.502

Gnomad4 ASJ exome AF: 0.568

Gnomad4 EAS exome AF: 0.227

Gnomad4 SAS exome AF: 0.588

Gnomad4 FIN exome AF: 0.625

Gnomad4 NFE exome AF: 0.651

Gnomad4 OTH exome AF: 0.560

GnomAD4 genome AF: 0.467 AC: 70895 AN: 151850 Hom.: 19670 Cov.: 31 AF XY: 0.467 AC XY: 34670 AN XY: 74210

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.522

Alfa AF: 0.579 Hom.: 11388

Bravo AF: 0.441

Asia WGS AF: 0.357 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2851097; hg19: chr11-74842197;