rs2741762

Variant names:

• chr11-6871635-G-A
• rs2741762
• NM_001004460.2:c.*969G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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]

ENSG00000283415 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004460.2. 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
	OR10A2	NM_001004460.2	MANE Select	c.*969G>A		3_prime_UTR	Exon 2 of 2	NP_001004460.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR10A2	ENST00000641461.1	MANE Select	c.*969G>A		3_prime_UTR	Exon 2 of 2	ENSP00000493131.1
	ENSG00000283415	ENST00000637205.2	TSL:5	n.606-20817C>T		intron	N/A
	ENSG00000283415	ENST00000767881.1		n.215-7335C>T		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.352 AC: 14550 AN: 41378

American (AMR) AF: 0.622 AC: 9508 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2123 AN: 3468

East Asian (EAS) AF: 0.711 AC: 3667 AN: 5160

South Asian (SAS) AF: 0.587 AC: 2820 AN: 4806

European-Finnish (FIN) AF: 0.622 AC: 6568 AN: 10560

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41944 AN: 67966

Other (OTH) AF: 0.559 AC: 1180 AN: 2112

Alfa AF: 0.603 Hom.: 50090

Bravo AF: 0.539

Asia WGS AF: 0.626 AC: 2176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.63
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2741762; hg19: chr11-6892866;