11-58292720-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 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: Benign. The variant received -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.

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>A		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.442 AC: 6720 AN: 15190

American (AMR) AF: 0.204 AC: 7909 AN: 38720

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 2709 AN: 15600

East Asian (EAS) AF: 0.179 AC: 3353 AN: 18770

South Asian (SAS) AF: 0.206 AC: 14660 AN: 71262

European-Finnish (FIN) AF: 0.242 AC: 9039 AN: 37318

Middle Eastern (MID) AF: 0.246 AC: 875 AN: 3558

European-Non Finnish (NFE) AF: 0.189 AC: 70708 AN: 374754

Other (OTH) AF: 0.195 AC: 5237 AN: 26842

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

African (AFR) AF: 0.452 AC: 18704 AN: 41370

American (AMR) AF: 0.242 AC: 3695 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 636 AN: 3468

East Asian (EAS) AF: 0.176 AC: 903 AN: 5120

South Asian (SAS) AF: 0.190 AC: 912 AN: 4806

European-Finnish (FIN) AF: 0.255 AC: 2690 AN: 10534

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.198 AC: 13480 AN: 67958

Other (OTH) AF: 0.257 AC: 544 AN: 2116

Alfa AF: 0.221 Hom.: 6843

Bravo AF: 0.282

Asia WGS AF: 0.158 AC: 549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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