rs10491216

Positions:

• chr17-3417112-C-T

Variant summary

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

The NM_012373.3(OR3A3):​c.-6-3468C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 151,760 control chromosomes in the GnomAD database, including 2,693 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 0.18 (2693 hom., cov: 32)
• Consequence: OR3A3 NM_012373.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.789

Genes affected

OR3A3 (HGNC:8284): (olfactory receptor family 3 subfamily A member 3) 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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR3A3	NM_012373.3	c.-6-3468C>T		intron_variant		ENST00000641141.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR3A3	ENST00000641141.1	c.-6-3468C>T		intron_variant			NM_012373.3	P1

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27172 AN: 151640 Hom.: 2692 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.179 AC: 27175 AN: 151760 Hom.: 2693 Cov.: 32 AF XY: 0.186 AC XY: 13783 AN XY: 74176

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.186

Alfa AF: 0.172 Hom.: 4757

Bravo AF: 0.174

Asia WGS AF: 0.301 AC: 1044 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491216; hg19: chr17-3320406;