11-6863532-C-T

Variant names:

• chr11-6863532-C-T
• rs2595456
• NM_001004460.2:c.-133+181C>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.-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
• Publications: 4 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.465 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR10A2	NM_001004460.2	MANE Select	c.-133+181C>T		intron	N/A	NP_001004460.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR10A2	ENST00000641461.1	MANE Select	c.-133+181C>T		intron	N/A	ENSP00000493131.1
	ENSG00000283415	ENST00000637205.2	TSL:5	n.606-12714G>A		intron	N/A

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

African (AFR) AF: 0.322 AC: 13279 AN: 41278

American (AMR) AF: 0.354 AC: 5395 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1821 AN: 3466

East Asian (EAS) AF: 0.356 AC: 1825 AN: 5130

South Asian (SAS) AF: 0.421 AC: 2019 AN: 4794

European-Finnish (FIN) AF: 0.500 AC: 5247 AN: 10484

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31840 AN: 67880

Other (OTH) AF: 0.449 AC: 944 AN: 2104

Alfa AF: 0.401 Hom.: 2268

Bravo AF: 0.401

Asia WGS AF: 0.374 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.15
PhyloP100		-1.5
PromoterAI		0.0034	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2595456; hg19: chr11-6884763;