rs17197261

chr14-21570031-A-Cchr14-21570031-A-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001005465.2(OR10G3):c.714T>G(p.Ala238=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,614,158 control chromosomes in the GnomAD database, including 13,482 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 0.097 (1178 hom., cov: 32)
  • Exomes 𝑓: 0.12 (12304 hom.)
• Consequence: OR10G3 NM_001005465.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

OR10G3 (HGNC:8171): (olfactory receptor family 10 subfamily G 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BP7: Synonymous conserved (PhyloP=-1.2 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR10G3	NM_001005465.2	c.714T>G	p.Ala238=	synonymous_variant	2/2	ENST00000641040.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR10G3	ENST00000641040.1	c.714T>G	p.Ala238=	synonymous_variant	2/2		NM_001005465.2	P1
OR10G3	ENST00000641185.1	c.714T>G	p.Ala238=	synonymous_variant	3/3			P1
OR10G3	ENST00000641655.1	n.342T>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.0972 AC: 14792 AN: 152174 Hom.: 1173 Cov.: 32

Gnomad AFR AF: 0.0248

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.0308

Gnomad SAS AF: 0.0569

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.0962

GnomAD3 exomes AF: 0.127 AC: 31789 AN: 251224 Hom.: 3400 AF XY: 0.118 AC XY: 15999 AN XY: 135750

Gnomad AFR exome AF: 0.0233

Gnomad AMR exome AF: 0.353

Gnomad ASJ exome AF: 0.0804

Gnomad EAS exome AF: 0.0331

Gnomad SAS exome AF: 0.0516

Gnomad FIN exome AF: 0.0682

Gnomad NFE exome AF: 0.123

Gnomad OTH exome AF: 0.130

GnomAD4 exome AF: 0.119 AC: 173451 AN: 1461866 Hom.: 12304 Cov.: 47 AF XY: 0.116 AC XY: 84518 AN XY: 727226

Gnomad4 AFR exome AF: 0.0201

Gnomad4 AMR exome AF: 0.343

Gnomad4 ASJ exome AF: 0.0821

Gnomad4 EAS exome AF: 0.0184

Gnomad4 SAS exome AF: 0.0518

Gnomad4 FIN exome AF: 0.0729

Gnomad4 NFE exome AF: 0.125

Gnomad4 OTH exome AF: 0.110

GnomAD4 genome AF: 0.0972 AC: 14807 AN: 152292 Hom.: 1178 Cov.: 32 AF XY: 0.0966 AC XY: 7192 AN XY: 74474

Gnomad4 AFR AF: 0.0248

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.0309

Gnomad4 SAS AF: 0.0580

Gnomad4 FIN AF: 0.0653

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.0947

Alfa AF: 0.114 Hom.: 1529

Bravo AF: 0.109

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	7.1
Dann	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs17197261; hg19: chr14-22038162; COSMIC: COSV57809749; COSMIC: COSV57809749;