Variant rs2427808 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001004478.2(OR10Z1):c.939A>T(p.Gly313Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 1,609,288 control chromosomes in the GnomAD database, including 12,861 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 0.10 ( 875 hom., cov: 32)

Exomes 𝑓: 0.12 ( 11986 hom. )

Consequence

OR10Z1
NM_001004478.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00600

Variant links:

Genes affected

OR10Z1 (HGNC:14996): (olfactory receptor family 10 subfamily Z 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]

OR10Z1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP7

Synonymous conserved (PhyloP=-0.006 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR10Z1	NM_001004478.2 linkuse as main transcript	c.939A>T	p.Gly313Gly	synonymous_variant	2/2	ENST00000641002.1	NP_001004478.1	Q8NGY1A0A126GV63

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR10Z1	ENST00000641002.1 linkuse as main transcript	c.939A>T	p.Gly313Gly	synonymous_variant	2/2		NM_001004478.2	ENSP00000493003.1		Q8NGY1

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15788

AN:

152072

Hom.:

871

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0642

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.111

Gnomad ASJ

AF:

0.0686

Gnomad EAS

AF:

0.0895

Gnomad SAS

AF:

0.200

Gnomad FIN

AF:

0.0707

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.127

Gnomad OTH

AF:

0.105

GnomAD3 exomes

AF:

0.120

AC:

29754

AN:

248258

Hom.:

2038

AF XY:

0.126

AC XY:

16831

AN XY:

134006

show subpopulations

Gnomad AFR exome

AF:

0.0670

Gnomad AMR exome

AF:

0.0993

Gnomad ASJ exome

AF:

0.0728

Gnomad EAS exome

AF:

0.0872

Gnomad SAS exome

AF:

0.206

Gnomad FIN exome

AF:

0.0686

Gnomad NFE exome

AF:

0.130

Gnomad OTH exome

AF:

0.114

GnomAD4 exome

AF:

0.125

AC:

181836

AN:

1457098

Hom.:

11986

Cov.:

AF XY:

0.128

AC XY:

92638

AN XY:

724870

show subpopulations

Gnomad4 AFR exome

AF:

0.0651

Gnomad4 AMR exome

AF:

0.0993

Gnomad4 ASJ exome

AF:

0.0719

Gnomad4 EAS exome

AF:

0.118

Gnomad4 SAS exome

AF:

0.206

Gnomad4 FIN exome

AF:

0.0738

Gnomad4 NFE exome

AF:

0.126

Gnomad4 OTH exome

AF:

0.117

GnomAD4 genome

AF:

0.104

AC:

15802

AN:

152190

Hom.:

875

Cov.:

AF XY:

0.103

AC XY:

7630

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.0642

Gnomad4 AMR

AF:

0.112

Gnomad4 ASJ

AF:

0.0686

Gnomad4 EAS

AF:

0.0893

Gnomad4 SAS

AF:

0.200

Gnomad4 FIN

AF:

0.0707

Gnomad4 NFE

AF:

0.127

Gnomad4 OTH

AF:

0.105

Alfa

AF:

0.113

Hom.:

338

Bravo

AF:

0.102

Asia WGS

AF:

0.137

AC:

477

AN:

3478

EpiCase

AF:

0.123

EpiControl

AF:

0.127

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

3.4

DANN

Benign

0.67

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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