17-3351681-A-G

Position:

• chr17-3351681-A-G

Variant summary

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

The NM_002551.5(OR3A2):​c.-376-15555T>C variant causes a intron change. 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 0.40 (11278 hom., cov: 20)
• Consequence: OR3A2 NM_002551.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

OR3A2 (HGNC:8283): (olfactory receptor family 3 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]

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 (AMR) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR3A2	NM_002551.5	c.-376-15555T>C		intron_variant			NP_002542.4
OR3A2	XM_047436157.1	c.-626-15555T>C		intron_variant			XP_047292113.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR3A2	ENST00000573901.3	c.-376-15555T>C		intron_variant		3		ENSP00000516654.1
OR3A2	ENST00000573491.5	c.-178-15555T>C		intron_variant		3		ENSP00000493118.1
OR3A2	ENST00000576166.2	c.-178-15555T>C		intron_variant		5		ENSP00000493095.1

Frequencies

GnomAD3 genomes AF: 0.399 AC: 57228 AN: 143308 Hom.: 11265 Cov.: 20

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.463

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.399 AC: 57270 AN: 143404 Hom.: 11278 Cov.: 20 AF XY: 0.406 AC XY: 28161 AN XY: 69390

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.399

Alfa AF: 0.396 Hom.: 1197

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.0
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs230463; hg19: chr17-3254975;