rs2851097

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr11-75131152-C-G
• chr11-75131152-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000525935.1(OR2AT1P):​n.729G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2AT1P		n.75131152C>G		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 289616 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 150758

African (AFR) AF: 0.00 AC: 0 AN: 7868

American (AMR) AF: 0.00 AC: 0 AN: 13088

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9046

East Asian (EAS) AF: 0.00 AC: 0 AN: 21298

South Asian (SAS) AF: 0.00 AC: 0 AN: 9320

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 35642

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2862

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 173360

Other (OTH) AF: 0.00 AC: 0 AN: 17132

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 12789

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.6
DANN	Benign	0.53
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;