11-75131152-C-T

Variant names:

• chr11-75131152-C-T
• rs2851097
• ENST00000525935.1:n.729G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000525935.1(OR2AT1P):​n.729G>A variant causes a non coding transcript exon 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: OR2AT1P ENST00000525935.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.846
• Publications: 6 publications found

Genes affected

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]

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]

ENSG00000255395 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
OR2AT1P	ENST00000525935.1	n.729G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
SLCO2B1	ENST00000531713.5	c.-51+30297C>T		intron_variant	Intron 1 of 3	3		ENSP00000432889.1
SLCO2B1	ENST00000526660.5	n.293+30297C>T		intron_variant	Intron 1 of 2	3

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

African (AFR) AF: 0.179 AC: 1408 AN: 7858

American (AMR) AF: 0.502 AC: 6562 AN: 13066

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 5134 AN: 9038

East Asian (EAS) AF: 0.227 AC: 4831 AN: 21286

South Asian (SAS) AF: 0.588 AC: 5465 AN: 9296

European-Finnish (FIN) AF: 0.625 AC: 22273 AN: 35620

Middle Eastern (MID) AF: 0.569 AC: 1624 AN: 2856

European-Non Finnish (NFE) AF: 0.651 AC: 112813 AN: 173194

Other (OTH) AF: 0.560 AC: 9589 AN: 17116

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

African (AFR) AF: 0.166 AC: 6872 AN: 41412

American (AMR) AF: 0.474 AC: 7226 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1859 AN: 3468

East Asian (EAS) AF: 0.240 AC: 1240 AN: 5162

South Asian (SAS) AF: 0.527 AC: 2534 AN: 4806

European-Finnish (FIN) AF: 0.607 AC: 6412 AN: 10566

Middle Eastern (MID) AF: 0.528 AC: 153 AN: 290

European-Non Finnish (NFE) AF: 0.631 AC: 42861 AN: 67872

Other (OTH) AF: 0.522 AC: 1102 AN: 2110

Alfa AF: 0.576 Hom.: 12789

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
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs2851097; hg19: chr11-74842197;