rs17197261

Variant names:

• chr14-21570031-A-C
• rs17197261
• NM_001005465.2:c.714T>G

Your query was ambiguous. Multiple possible variants found:

• chr14-21570031-A-C
• chr14-21570031-A-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001005465.2(OR10G3):​c.714T>G​(p.Ala238Ala) 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
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
OR10G3	NM_001005465.2	c.714T>G	p.Ala238Ala	synonymous_variant	Exon 2 of 2	ENST00000641040.1	NP_001005465.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR10G3	ENST00000641040.1	c.714T>G	p.Ala238Ala	synonymous_variant	Exon 2 of 2		NM_001005465.2	ENSP00000493245.1
OR10G3	ENST00000641185.1	c.714T>G	p.Ala238Ala	synonymous_variant	Exon 3 of 3			ENSP00000492973.1
OR10G3	ENST00000641655.1	n.342T>G		non_coding_transcript_exon_variant	Exon 2 of 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

GnomAD2 exomes AF: 0.127 AC: 31789 AN: 251224 AF XY: 0.118

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 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

African (AFR) AF: 0.0201 AC: 672 AN: 33480

American (AMR) AF: 0.343 AC: 15357 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.0821 AC: 2147 AN: 26136

East Asian (EAS) AF: 0.0184 AC: 730 AN: 39698

South Asian (SAS) AF: 0.0518 AC: 4464 AN: 86258

European-Finnish (FIN) AF: 0.0729 AC: 3894 AN: 53420

Middle Eastern (MID) AF: 0.0907 AC: 523 AN: 5768

European-Non Finnish (NFE) AF: 0.125 AC: 139003 AN: 1111992

Other (OTH) AF: 0.110 AC: 6661 AN: 60394

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

African (AFR) AF: 0.0248 AC: 1029 AN: 41570

American (AMR) AF: 0.239 AC: 3643 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 301 AN: 3472

East Asian (EAS) AF: 0.0309 AC: 160 AN: 5184

South Asian (SAS) AF: 0.0580 AC: 280 AN: 4826

European-Finnish (FIN) AF: 0.0653 AC: 694 AN: 10622

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.124 AC: 8429 AN: 68028

Other (OTH) AF: 0.0947 AC: 200 AN: 2112

Alfa AF: 0.115 Hom.: 1937

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
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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