dbSNP rs1788998: OR5G3:p.Gln6His (chr11-56820499-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000435756.2(OR5G3):c.18G>T(p.Gln6His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 397,950 control chromosomes in the GnomAD database, including 81,749 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/5 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.65 ( 32466 hom., cov: 31)

Exomes 𝑓: 0.63 ( 49283 hom. )

Consequence

OR5G3
ENST00000435756.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.300

Variant links:

Genes affected

OR5G3 (HGNC:15287): (olfactory receptor family 5 subfamily G member 3 (gene/pseudogene)) 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. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional. [provided by RefSeq, Jan 2017]

OR5G3 links:

ENSG00000290749 (HGNC:):

ENSG00000290749 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR5G3		n.56820499C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR5G3	ENST00000435756.2 link	c.18G>T	p.Gln6His	missense_variant	Exon 1 of 1	6		ENSP00000477337.2
ENSG00000290749	ENST00000627642.1 link	n.-77G>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.652

AC:

98887

AN:

151776

Hom.:

32421

Cov.:

show subpopulations

Gnomad AFR

AF:

0.671

Gnomad AMI

AF:

0.513

Gnomad AMR

AF:

0.646

Gnomad ASJ

AF:

0.551

Gnomad EAS

AF:

0.787

Gnomad SAS

AF:

0.814

Gnomad FIN

AF:

0.757

Gnomad MID

AF:

0.611

Gnomad NFE

AF:

0.610

Gnomad OTH

AF:

0.639

GnomAD3 exomes

AF:

0.455

AC:

AN:

Hom.:

AF XY:

0.375

AC XY:

AN XY:

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad NFE exome

AF:

0.625

GnomAD4 exome

AF:

0.631

AC:

155153

AN:

246056

Hom.:

49283

Cov.:

AF XY:

0.628

AC XY:

78248

AN XY:

124676

show subpopulations

Gnomad4 AFR exome

AF:

0.671

Gnomad4 AMR exome

AF:

0.666

Gnomad4 ASJ exome

AF:

0.541

Gnomad4 EAS exome

AF:

0.695

Gnomad4 SAS exome

AF:

0.824

Gnomad4 FIN exome

AF:

0.725

Gnomad4 NFE exome

AF:

0.606

Gnomad4 OTH exome

AF:

0.639

GnomAD4 genome

AF:

0.652

AC:

98994

AN:

151894

Hom.:

32466

Cov.:

AF XY:

0.660

AC XY:

48933

AN XY:

74190

show subpopulations

Gnomad4 AFR

AF:

0.672

Gnomad4 AMR

AF:

0.647

Gnomad4 ASJ

AF:

0.551

Gnomad4 EAS

AF:

0.787

Gnomad4 SAS

AF:

0.814

Gnomad4 FIN

AF:

0.757

Gnomad4 NFE

AF:

0.610

Gnomad4 OTH

AF:

0.643

Alfa

AF:

0.610

Hom.:

11124

Bravo

AF:

0.640

Asia WGS

AF:

0.806

AC:

2802

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

DANN

Benign

0.71

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over