Variant chr11-56701053-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_001005213.2(OR9G1):c.666C>A(p.Thr222=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00705 in 1,613,046 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0038 ( 0 hom., cov: 63)

Exomes 𝑓: 0.0074 ( 0 hom. )

Consequence

OR9G1
NM_001005213.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.88

Variant links:

Genes affected

OR9G1 (HGNC:15319): (olfactory receptor family 9 subfamily G 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]

OR9G1 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 11-56701053-C-A is Benign according to our data. Variant chr11-56701053-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 3250529.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.88 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR9G1	NM_001005213.2 linkuse as main transcript	c.666C>A	p.Thr222=	synonymous_variant	2/2	ENST00000642097.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR9G1	ENST00000642097.1 linkuse as main transcript	c.666C>A	p.Thr222=	synonymous_variant	2/2		NM_001005213.2	P1

Frequencies

GnomAD3 genomes

AF:

0.00376

AC:

571

AN:

151964

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00104

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00137

Gnomad ASJ

AF:

0.00578

Gnomad EAS

AF:

0.000384

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00889

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00556

Gnomad OTH

AF:

0.00192

GnomAD3 exomes

AF:

0.00579

AC:

1442

AN:

249058

Hom.:

AF XY:

0.00573

AC XY:

773

AN XY:

134818

show subpopulations

Gnomad AFR exome

AF:

0.00160

Gnomad AMR exome

AF:

0.00188

Gnomad ASJ exome

AF:

0.00745

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00127

Gnomad FIN exome

AF:

0.0126

Gnomad NFE exome

AF:

0.00832

Gnomad OTH exome

AF:

0.00604

GnomAD4 exome

AF:

0.00740

AC:

10809

AN:

1460964

Hom.:

Cov.:

200

AF XY:

0.00722

AC XY:

5246

AN XY:

726786

show subpopulations

Gnomad4 AFR exome

AF:

0.00143

Gnomad4 AMR exome

AF:

0.00170

Gnomad4 ASJ exome

AF:

0.00800

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00157

Gnomad4 FIN exome

AF:

0.0123

Gnomad4 NFE exome

AF:

0.00834

Gnomad4 OTH exome

AF:

0.00616

GnomAD4 genome

AF:

0.00375

AC:

571

AN:

152082

Hom.:

Cov.:

AF XY:

0.00374

AC XY:

278

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.00103

Gnomad4 AMR

AF:

0.00137

Gnomad4 ASJ

AF:

0.00578

Gnomad4 EAS

AF:

0.000385

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.00889

Gnomad4 NFE

AF:

0.00556

Gnomad4 OTH

AF:

0.00190

Alfa

AF:

0.00697

Hom.:

EpiCase

AF:

0.00856

EpiControl

AF:

0.00670

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jun 01, 2024

OR9G1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.6

DANN

Benign

0.36

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over