rs12289961

Variant names:

• chr11-58292720-C-G
• rs12289961
• ENST00000610280.1:n.46G>C

Your query was ambiguous. Multiple possible variants found:

• chr11-58292720-C-G
• chr11-58292720-C-T

Variant summary

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

The ENST00000610280.1(OR10Q2P):​n.46G>C 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 0.00000662 in 604,102 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 0.0000066 (0 hom.)
• Consequence: OR10Q2P ENST00000610280.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62
• Publications: 0 publications found

Genes affected

OR10Q2P (HGNC:15135): (olfactory receptor family 10 subfamily Q member 2 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]

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=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000610280.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR10Q2P	ENST00000610280.1	TSL:6	n.46G>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000662 AC: 4 AN: 604102 Hom.: 0 Cov.: 8 AF XY: 0.00000307 AC XY: 1 AN XY: 325456

African (AFR) AF: 0.00 AC: 0 AN: 15272

American (AMR) AF: 0.00 AC: 0 AN: 38776

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15662

East Asian (EAS) AF: 0.00 AC: 0 AN: 18894

South Asian (SAS) AF: 0.00 AC: 0 AN: 71286

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 37446

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3574

European-Non Finnish (NFE) AF: 0.0000106 AC: 4 AN: 376208

Other (OTH) AF: 0.00 AC: 0 AN: 26984

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.4
DANN	Benign	0.63
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs12289961; hg19: chr11-58060192;