11-6863532-C-T

Variant summary

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

The NM_001004460.2(OR10A2):c.-133+181C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,572 control chromosomes in the GnomAD database, including 13,531 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 0.42 (13531 hom., cov: 27)
• Consequence: OR10A2 NM_001004460.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR10A2	NM_001004460.2	c.-133+181C>T		intron_variant		ENST00000641461.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR10A2	ENST00000641461.1	c.-133+181C>T		intron_variant			NM_001004460.2	P1
	ENST00000637205.2	n.606-12714G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63005 AN: 151454 Hom.: 13529 Cov.: 27

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.452

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.416 AC: 63018 AN: 151572 Hom.: 13531 Cov.: 27 AF XY: 0.416 AC XY: 30774 AN XY: 74046

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.449

Alfa AF: 0.404 Hom.: 2230

Bravo AF: 0.401

Asia WGS AF: 0.374 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.28
Dann	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2595456; hg19: chr11-6884763;