rs9898721

Positions:

• chr17-3304125-C-G

Variant summary

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

The ENST00000573901.3(OR3A2):​c.-278-19574G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 151,852 control chromosomes in the GnomAD database, including 2,962 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 0.17 (2962 hom., cov: 30)
• Consequence: OR3A2 ENST00000573901.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR3A2	NM_002551.5	c.-278-19574G>C		intron_variant		ENST00000573901.3	NP_002542.4
OR3A2	XM_047436157.1	c.-528-4279G>C		intron_variant			XP_047292113.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR3A2	ENST00000573901.3	c.-278-19574G>C		intron_variant		3	NM_002551.5	ENSP00000516654	P1
OR3A2	ENST00000573491.5	c.-84-24972G>C		intron_variant		3		ENSP00000493118
OR3A2	ENST00000576166.2	c.-84-24972G>C		intron_variant		5		ENSP00000493095

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25131 AN: 151740 Hom.: 2953 Cov.: 30

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0397

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0622

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0948

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.166 AC: 25172 AN: 151852 Hom.: 2962 Cov.: 30 AF XY: 0.162 AC XY: 12026 AN XY: 74200

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.0398

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0622

Gnomad4 NFE AF: 0.0948

Gnomad4 OTH AF: 0.175

Alfa AF: 0.135 Hom.: 230

Bravo AF: 0.180

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
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: rs9898721; hg19: chr17-3207419;