Variant 9-122614808-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_012364.1(OR1Q1):c.71A>G(p.Gln24Arg) variant causes a missense change. The variant allele was found at a frequency of 0.83 in 1,613,582 control chromosomes in the GnomAD database, including 558,812 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.79 ( 48405 hom., cov: 29)

Exomes 𝑓: 0.83 ( 510407 hom. )

Consequence

OR1Q1
NM_012364.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.87

Variant links:

Genes affected

OR1Q1 (HGNC:8223): (olfactory receptor family 1 subfamily Q member 1) 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]

OR1Q1 links:

ENSG00000234156 (HGNC:):

ENSG00000234156 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.3050108E-6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR1Q1	NM_012364.1 linkuse as main transcript	c.71A>G	p.Gln24Arg	missense_variant	1/1	ENST00000297913.3	NP_036496.1	Q15612
LOC124902265	XR_007061759.1 linkuse as main transcript	n.344+4758A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR1Q1	ENST00000297913.3 linkuse as main transcript	c.71A>G	p.Gln24Arg	missense_variant	1/1	6	NM_012364.1	ENSP00000297913.2		Q15612
ENSG00000234156	ENST00000431442.2 linkuse as main transcript	n.4767+4758A>G		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.794

AC:

120518

AN:

151856

Hom.:

48381

Cov.:

show subpopulations

Gnomad AFR

AF:

0.670

Gnomad AMI

AF:

0.880

Gnomad AMR

AF:

0.841

Gnomad ASJ

AF:

0.789

Gnomad EAS

AF:

0.945

Gnomad SAS

AF:

0.937

Gnomad FIN

AF:

0.896

Gnomad MID

AF:

0.756

Gnomad NFE

AF:

0.820

Gnomad OTH

AF:

0.785

GnomAD3 exomes

AF:

0.845

AC:

212517

AN:

251392

Hom.:

90443

AF XY:

0.848

AC XY:

115234

AN XY:

135866

show subpopulations

Gnomad AFR exome

AF:

0.664

Gnomad AMR exome

AF:

0.890

Gnomad ASJ exome

AF:

0.790

Gnomad EAS exome

AF:

0.942

Gnomad SAS exome

AF:

0.926

Gnomad FIN exome

AF:

0.885

Gnomad NFE exome

AF:

0.819

Gnomad OTH exome

AF:

0.827

GnomAD4 exome

AF:

0.834

AC:

1219254

AN:

1461608

Hom.:

510407

Cov.:

AF XY:

0.836

AC XY:

607906

AN XY:

727134

show subpopulations

Gnomad4 AFR exome

AF:

0.658

Gnomad4 AMR exome

AF:

0.886

Gnomad4 ASJ exome

AF:

0.792

Gnomad4 EAS exome

AF:

0.956

Gnomad4 SAS exome

AF:

0.926

Gnomad4 FIN exome

AF:

0.884

Gnomad4 NFE exome

AF:

0.825

Gnomad4 OTH exome

AF:

0.823

GnomAD4 genome

AF:

0.794

AC:

120593

AN:

151974

Hom.:

48405

Cov.:

AF XY:

0.804

AC XY:

59756

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.670

Gnomad4 AMR

AF:

0.841

Gnomad4 ASJ

AF:

0.789

Gnomad4 EAS

AF:

0.944

Gnomad4 SAS

AF:

0.937

Gnomad4 FIN

AF:

0.896

Gnomad4 NFE

AF:

0.820

Gnomad4 OTH

AF:

0.785

Alfa

AF:

0.812

Hom.:

124102

Bravo

AF:

0.782

TwinsUK

AF:

0.831

AC:

3080

ALSPAC

AF:

0.827

AC:

3186

ESP6500AA

AF:

0.670

AC:

2951

ESP6500EA

AF:

0.819

AC:

7047

ExAC

AF:

0.839

AC:

101904

Asia WGS

AF:

0.893

AC:

3106

AN:

3478

EpiCase

AF:

0.807

EpiControl

AF:

0.797

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.79

BayesDel_noAF

Benign

-0.76

CADD

Benign

DANN

Benign

0.96

DEOGEN2

Benign

0.039

Eigen

Benign

-0.86

Eigen_PC

Benign

-0.83

FATHMM_MKL

Benign

0.24

LIST_S2

Benign

0.11

MetaRNN

Benign

0.0000013

MetaSVM

Benign

-0.98

MutationAssessor

Benign

1.3

PrimateAI

Benign

0.17

PROVEAN

Uncertain

-2.4

REVEL

Benign

0.092

Sift

Benign

0.070

Sift4G

Uncertain

0.027

Polyphen

0.0020

Vest4

0.053

MPC

0.15

ClinPred

0.015

GERP RS

2.9

Varity_R

0.15

gMVP

0.31

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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