rs9898721

Variant names:

• chr17-3304125-C-G
• rs9898721
• NM_002551.5:c.-278-19574G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002551.5(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 NM_002551.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002551.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR3A2	NM_002551.5	MANE Select	c.-278-19574G>C		intron	N/A	NP_002542.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR3A2	ENST00000573901.3	TSL:3 MANE Select	c.-278-19574G>C		intron	N/A	ENSP00000516654.1
	OR3A2	ENST00000573491.5	TSL:3	c.-84-24972G>C		intron	N/A	ENSP00000493118.1
	OR3A2	ENST00000576166.2	TSL:5	c.-84-24972G>C		intron	N/A	ENSP00000493095.1

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

African (AFR) AF: 0.333 AC: 13753 AN: 41336

American (AMR) AF: 0.166 AC: 2539 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3468

East Asian (EAS) AF: 0.0398 AC: 206 AN: 5176

South Asian (SAS) AF: 0.114 AC: 550 AN: 4814

European-Finnish (FIN) AF: 0.0622 AC: 655 AN: 10526

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0948 AC: 6446 AN: 67978

Other (OTH) AF: 0.175 AC: 368 AN: 2100

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.39
PhyloP100		0.076
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs9898721; hg19: chr17-3207419;