11-75131152-C-T

Variant names:

• chr11-75131152-C-T
• rs2851097
• ENST00000531713.5:c.-51+30297C>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:15145): (olfactory receptor family 2 subfamily AT member 1 pseudogene) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]

ENSG00000255395 (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 rank	MANE	Protein	UniProt
OR2AT1P		n.75131152C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO2B1	ENST00000531713.5	c.-51+30297C>T		intron_variant	Intron 1 of 3	3		ENSP00000432889.1
OR2AT1P	ENST00000525935.1	n.729G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
SLCO2B1	ENST00000526660.5	n.293+30297C>T		intron_variant	Intron 1 of 2	3
ENSG00000255395	ENST00000530550.1	n.175+2667G>A		intron_variant	Intron 2 of 3	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;