rs1788998

Variant names:

• chr11-56820499-C-A
• rs1788998
• ENST00000435756.2:c.18G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-56820499-C-A
• chr11-56820499-C-G
• chr11-56820499-C-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 2 publications found

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]

ENSG00000290749 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	c.18G>T	p.Gln6His	missense_variant	Exon 1 of 1	6		ENSP00000477337.2
ENSG00000290749	ENST00000627642.1	n.-77G>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.652 AC: 98887 AN: 151776 Hom.: 32421 Cov.: 31

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

GnomAD2 exomes AF: 0.455 AC: 10 AN: 22 AF XY: 0.375

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.: 0 AF XY: 0.628 AC XY: 78248 AN XY: 124676

African (AFR) AF: 0.671 AC: 4799 AN: 7156

American (AMR) AF: 0.666 AC: 4945 AN: 7422

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 4988 AN: 9222

East Asian (EAS) AF: 0.695 AC: 15906 AN: 22886

South Asian (SAS) AF: 0.824 AC: 2498 AN: 3030

European-Finnish (FIN) AF: 0.725 AC: 15100 AN: 20824

Middle Eastern (MID) AF: 0.629 AC: 810 AN: 1288

European-Non Finnish (NFE) AF: 0.606 AC: 95661 AN: 157870

Other (OTH) AF: 0.639 AC: 10446 AN: 16358

GnomAD4 genome AF: 0.652 AC: 98994 AN: 151894 Hom.: 32466 Cov.: 31 AF XY: 0.660 AC XY: 48933 AN XY: 74190

African (AFR) AF: 0.672 AC: 27818 AN: 41412

American (AMR) AF: 0.647 AC: 9866 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1910 AN: 3468

East Asian (EAS) AF: 0.787 AC: 4047 AN: 5144

South Asian (SAS) AF: 0.814 AC: 3921 AN: 4816

European-Finnish (FIN) AF: 0.757 AC: 7993 AN: 10556

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41434 AN: 67934

Other (OTH) AF: 0.643 AC: 1357 AN: 2110

Alfa AF: 0.610 Hom.: 12688

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	15
DANN	Benign	0.71
PhyloP100		-0.30

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: rs1788998; hg19: chr11-56587975;