Variant rs7934354 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001005289.5(OR52H1):c.830T>C(p.Met277Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0438 in 1,613,792 control chromosomes in the GnomAD database, including 6,349 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 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 0.077 ( 979 hom., cov: 32)

Exomes 𝑓: 0.040 ( 5370 hom. )

Consequence

OR52H1
NM_001005289.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.27

Variant links:

Genes affected

OR52H1 (HGNC:15218): (olfactory receptor family 52 subfamily H 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]

OR52H1 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=0.0040930808).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR52H1	NM_001005289.5 linkuse as main transcript	c.830T>C	p.Met277Thr	missense_variant	2/2	ENST00000322653.7	NP_001005289.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR52H1	ENST00000322653.7 linkuse as main transcript	c.830T>C	p.Met277Thr	missense_variant	2/2		NM_001005289.5	ENSP00000326259	P1
OR52H1	ENST00000641796.2 linkuse as main transcript	c.830T>C	p.Met277Thr	missense_variant	1/1			ENSP00000493308	P1

Frequencies

GnomAD3 genomes

AF:

0.0774

AC:

11752

AN:

151898

Hom.:

979

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.0869

Gnomad ASJ

AF:

0.0386

Gnomad EAS

AF:

0.389

Gnomad SAS

AF:

0.132

Gnomad FIN

AF:

0.0539

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0161

Gnomad OTH

AF:

0.0670

GnomAD3 exomes

AF:

0.0809

AC:

20330

AN:

251442

Hom.:

1926

AF XY:

0.0778

AC XY:

10572

AN XY:

135892

show subpopulations

Gnomad AFR exome

AF:

0.145

Gnomad AMR exome

AF:

0.103

Gnomad ASJ exome

AF:

0.0361

Gnomad EAS exome

AF:

0.360

Gnomad SAS exome

AF:

0.120

Gnomad FIN exome

AF:

0.0588

Gnomad NFE exome

AF:

0.0186

Gnomad OTH exome

AF:

0.0637

GnomAD4 exome

AF:

0.0403

AC:

58886

AN:

1461776

Hom.:

5370

Cov.:

AF XY:

0.0419

AC XY:

30485

AN XY:

727206

show subpopulations

Gnomad4 AFR exome

AF:

0.155

Gnomad4 AMR exome

AF:

0.100

Gnomad4 ASJ exome

AF:

0.0376

Gnomad4 EAS exome

AF:

0.414

Gnomad4 SAS exome

AF:

0.118

Gnomad4 FIN exome

AF:

0.0549

Gnomad4 NFE exome

AF:

0.0133

Gnomad4 OTH exome

AF:

0.0595

GnomAD4 genome

AF:

0.0774

AC:

11772

AN:

152016

Hom.:

979

Cov.:

AF XY:

0.0821

AC XY:

6099

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.140

Gnomad4 AMR

AF:

0.0869

Gnomad4 ASJ

AF:

0.0386

Gnomad4 EAS

AF:

0.389

Gnomad4 SAS

AF:

0.131

Gnomad4 FIN

AF:

0.0539

Gnomad4 NFE

AF:

0.0161

Gnomad4 OTH

AF:

0.0687

Alfa

AF:

0.0333

Hom.:

659

Bravo

AF:

0.0867

TwinsUK

AF:

0.0105

AC:

ALSPAC

AF:

0.0127

AC:

ESP6500AA

AF:

0.139

AC:

611

ESP6500EA

AF:

0.0199

AC:

171

ExAC

AF:

0.0817

AC:

9918

Asia WGS

AF:

0.252

AC:

874

AN:

3478

EpiCase

AF:

0.0192

EpiControl

AF:

0.0190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.65

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.0095

T;.

Eigen

Benign

-0.11

Eigen_PC

Benign

-0.022

FATHMM_MKL

Benign

0.54

LIST_S2

Benign

0.78

T;T

MetaRNN

Benign

0.0041

T;T

MetaSVM

Benign

-0.90

MutationAssessor

Benign

1.3

L;.

MutationTaster

Benign

1.1e-22

P;P

PrimateAI

Benign

0.21

REVEL

Benign

0.16

Polyphen

0.46

P;.

MPC

0.027

ClinPred

0.058

GERP RS

5.2

Varity_R

0.69

gMVP

0.27

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

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