rs2741762

Positions:

• chr11-6871635-G-A
• chr11-6871635-G-C
• chr11-6871635-G-T

Variant summary

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

The NM_001004460.2(OR10A2):​c.*969G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 151,924 control chromosomes in the GnomAD database, including 23,912 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 0.55 (23912 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: OR10A2 NM_001004460.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

Genes affected

OR10A2 (HGNC:8161): (olfactory receptor family 10 subfamily A member 2) 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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR10A2	NM_001004460.2	c.*969G>A		3_prime_UTR_variant	2/2	ENST00000641461.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR10A2	ENST00000641461.1	c.*969G>A		3_prime_UTR_variant	2/2		NM_001004460.2	P1
	ENST00000637205.2	n.606-20817C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83027 AN: 151804 Hom.: 23909 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.547 AC: 83072 AN: 151924 Hom.: 23912 Cov.: 32 AF XY: 0.548 AC XY: 40732 AN XY: 74264

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.559

Alfa AF: 0.609 Hom.: 37508

Bravo AF: 0.539

Asia WGS AF: 0.626 AC: 2176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2741762; hg19: chr11-6892866;