Variant rs61729907 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001005191.3(OR7D4):c.262C>T(p.Arg88Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 1,613,596 control chromosomes in the GnomAD database, including 24,793 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 0.15 ( 2009 hom., cov: 32)

Exomes 𝑓: 0.17 ( 22784 hom. )

Consequence

OR7D4
NM_001005191.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.74

Variant links:

Genes affected

OR7D4 (HGNC:8380): (olfactory receptor family 7 subfamily D member 4) 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]

OR7D4 links:

OR7E24 (HGNC:):

OR7E24 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 (MetaRNN=0.007482052).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR7D4	NM_001005191.3 linkuse as main transcript	c.262C>T	p.Arg88Trp	missense_variant	2/2	ENST00000641669.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Appris
OR7D4	ENST00000641669.1 linkuse as main transcript	c.262C>T	p.Arg88Trp	missense_variant	2/2	NM_001005191.3	P1
OR7D4	ENST00000308682.3 linkuse as main transcript	c.262C>T	p.Arg88Trp	missense_variant	1/1		P1
OR7D4	ENST00000641244.1 linkuse as main transcript	c.262C>T	p.Arg88Trp	missense_variant	2/2		P1

Frequencies

GnomAD3 genomes

AF:

0.151

AC:

23011

AN:

152020

Hom.:

2009

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0760

Gnomad AMI

AF:

0.183

Gnomad AMR

AF:

0.126

Gnomad ASJ

AF:

0.198

Gnomad EAS

AF:

0.227

Gnomad SAS

AF:

0.182

Gnomad FIN

AF:

0.253

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.176

Gnomad OTH

AF:

0.171

GnomAD3 exomes

AF:

0.170

AC:

42862

AN:

251422

Hom.:

4008

AF XY:

0.175

AC XY:

23822

AN XY:

135872

show subpopulations

Gnomad AFR exome

AF:

0.0741

Gnomad AMR exome

AF:

0.0906

Gnomad ASJ exome

AF:

0.208

Gnomad EAS exome

AF:

0.226

Gnomad SAS exome

AF:

0.192

Gnomad FIN exome

AF:

0.250

Gnomad NFE exome

AF:

0.175

Gnomad OTH exome

AF:

0.174

GnomAD4 exome

AF:

0.174

AC:

253564

AN:

1461458

Hom.:

22784

Cov.:

AF XY:

0.174

AC XY:

126750

AN XY:

727056

show subpopulations

Gnomad4 AFR exome

AF:

0.0735

Gnomad4 AMR exome

AF:

0.0936

Gnomad4 ASJ exome

AF:

0.204

Gnomad4 EAS exome

AF:

0.232

Gnomad4 SAS exome

AF:

0.188

Gnomad4 FIN exome

AF:

0.244

Gnomad4 NFE exome

AF:

0.172

Gnomad4 OTH exome

AF:

0.180

GnomAD4 genome

AF:

0.151

AC:

23011

AN:

152138

Hom.:

2009

Cov.:

AF XY:

0.156

AC XY:

11579

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.0758

Gnomad4 AMR

AF:

0.126

Gnomad4 ASJ

AF:

0.198

Gnomad4 EAS

AF:

0.226

Gnomad4 SAS

AF:

0.182

Gnomad4 FIN

AF:

0.253

Gnomad4 NFE

AF:

0.176

Gnomad4 OTH

AF:

0.174

Alfa

AF:

0.164

Hom.:

931

Bravo

AF:

0.137

TwinsUK

AF:

0.161

AC:

598

ALSPAC

AF:

0.170

AC:

655

ESP6500AA

AF:

0.0794

AC:

350

ESP6500EA

AF:

0.183

AC:

1572

ExAC

AF:

0.169

AC:

20510

Asia WGS

AF:

0.193

AC:

670

AN:

3478

EpiCase

AF:

0.181

EpiControl

AF:

0.185

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.095

BayesDel_addAF

Benign

-0.79

BayesDel_noAF

Benign

-0.76

Cadd

Benign

Dann

Uncertain

0.99

DEOGEN2

Benign

0.0073

T;T;T

Eigen

Benign

-0.68

Eigen_PC

Benign

-0.85

FATHMM_MKL

Benign

0.028

MetaRNN

Benign

0.0075

T;T;T

MetaSVM

Benign

-0.91

MutationAssessor

Benign

0.74

N;N;N

MutationTaster

Benign

1.0

PrimateAI

Benign

0.17

Polyphen

0.84

P;P;P

Vest4

0.037

MPC

0.071

ClinPred

0.033

GERP RS

0.41

Varity_R

0.12

gMVP

0.071

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