rs12289961

Positions:

• chr11-58292720-C-T

Variant summary

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

The ENST00000610280.1(OR10Q2P):​n.46G>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 0.216 in 753,866 control chromosomes in the GnomAD database, including 20,011 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 0.28 (6688 hom., cov: 31)
  • Exomes 𝑓: 0.20 (13323 hom.)
• Consequence: OR10Q2P ENST00000610280.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR10Q2P	ENST00000610280.1	n.46G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41768 AN: 151734 Hom.: 6683 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.258

GnomAD4 exome AF: 0.201 AC: 121210 AN: 602014 Hom.: 13323 Cov.: 8 AF XY: 0.201 AC XY: 65355 AN XY: 324462

Gnomad4 AFR exome AF: 0.442

Gnomad4 AMR exome AF: 0.204

Gnomad4 ASJ exome AF: 0.174

Gnomad4 EAS exome AF: 0.179

Gnomad4 SAS exome AF: 0.206

Gnomad4 FIN exome AF: 0.242

Gnomad4 NFE exome AF: 0.189

Gnomad4 OTH exome AF: 0.195

GnomAD4 genome AF: 0.275 AC: 41801 AN: 151852 Hom.: 6688 Cov.: 31 AF XY: 0.275 AC XY: 20413 AN XY: 74200

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.257

Alfa AF: 0.230 Hom.: 1138

Bravo AF: 0.282

Asia WGS AF: 0.158 AC: 549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12289961; hg19: chr11-58060192;