chr17-3417112-C-T

Variant names:

• chr17-3417112-C-T
• rs10491216
• NM_012373.3:c.-6-3468C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012373.3. 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
	OR3A3	NM_012373.3	MANE Select	c.-6-3468C>T		intron	N/A	NP_036505.3	A0A126GWB3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR3A3	ENST00000641141.1	MANE Select	c.-6-3468C>T		intron	N/A	ENSP00000493061.1	A0A126GWB3

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

African (AFR) AF: 0.133 AC: 5515 AN: 41370

American (AMR) AF: 0.214 AC: 3266 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 390 AN: 3470

East Asian (EAS) AF: 0.357 AC: 1844 AN: 5172

South Asian (SAS) AF: 0.230 AC: 1105 AN: 4814

European-Finnish (FIN) AF: 0.266 AC: 2796 AN: 10528

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.172 AC: 11652 AN: 67844

Other (OTH) AF: 0.186 AC: 392 AN: 2108

Alfa AF: 0.173 Hom.: 9735

Bravo AF: 0.174

Asia WGS AF: 0.301 AC: 1044 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.39
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs10491216; hg19: chr17-3320406;