Variant rs7927370 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001005275.2(OR4A15):c.770C>T(p.Ala257Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0535 in 1,613,406 control chromosomes in the GnomAD database, including 2,678 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 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 0.040 ( 184 hom., cov: 32)

Exomes 𝑓: 0.055 ( 2494 hom. )

Consequence

OR4A15
NM_001005275.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.78

Variant links:

Genes affected

OR4A15 (HGNC:15152): (olfactory receptor family 4 subfamily A member 15) 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]

OR4A15 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR4A15	NM_001005275.2 linkuse as main transcript	c.770C>T	p.Ala257Val	missense_variant	1/1	ENST00000641526.1	NP_001005275.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR4A15	ENST00000641526.1 linkuse as main transcript	c.770C>T	p.Ala257Val	missense_variant	1/1		NM_001005275.2	ENSP00000493060	P1

Frequencies

GnomAD3 genomes

AF:

0.0404

AC:

6144

AN:

152042

Hom.:

184

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00949

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0384

Gnomad ASJ

AF:

0.0231

Gnomad EAS

AF:

0.000581

Gnomad SAS

AF:

0.0420

Gnomad FIN

AF:

0.0538

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0617

Gnomad OTH

AF:

0.0476

GnomAD3 exomes

AF:

0.0448

AC:

11236

AN:

250930

Hom.:

336

AF XY:

0.0461

AC XY:

6245

AN XY:

135610

show subpopulations

Gnomad AFR exome

AF:

0.00855

Gnomad AMR exome

AF:

0.0253

Gnomad ASJ exome

AF:

0.0218

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0384

Gnomad FIN exome

AF:

0.0609

Gnomad NFE exome

AF:

0.0634

Gnomad OTH exome

AF:

0.0540

GnomAD4 exome

AF:

0.0549

AC:

80210

AN:

1461246

Hom.:

2494

Cov.:

AF XY:

0.0547

AC XY:

39795

AN XY:

726928

show subpopulations

Gnomad4 AFR exome

AF:

0.00843

Gnomad4 AMR exome

AF:

0.0255

Gnomad4 ASJ exome

AF:

0.0216

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0382

Gnomad4 FIN exome

AF:

0.0644

Gnomad4 NFE exome

AF:

0.0614

Gnomad4 OTH exome

AF:

0.0511

GnomAD4 genome

AF:

0.0404

AC:

6143

AN:

152160

Hom.:

184

Cov.:

AF XY:

0.0396

AC XY:

2948

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.00946

Gnomad4 AMR

AF:

0.0383

Gnomad4 ASJ

AF:

0.0231

Gnomad4 EAS

AF:

0.000582

Gnomad4 SAS

AF:

0.0423

Gnomad4 FIN

AF:

0.0538

Gnomad4 NFE

AF:

0.0617

Gnomad4 OTH

AF:

0.0471

Alfa

AF:

0.0541

Hom.:

570

Bravo

AF:

0.0368

TwinsUK

AF:

0.0545

AC:

202

ALSPAC

AF:

0.0602

AC:

232

ESP6500AA

AF:

0.00909

AC:

ESP6500EA

AF:

0.0609

AC:

523

ExAC

AF:

0.0455

AC:

5521

Asia WGS

AF:

0.0200

AC:

AN:

3478

EpiCase

AF:

0.0599

EpiControl

AF:

0.0571

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.097

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.77

CADD

Benign

DANN

Benign

0.068

DEOGEN2

Benign

0.0085

T;.

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.0035

LIST_S2

Benign

0.36

T;T

MetaRNN

Benign

0.0030

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.93

N;.

MutationTaster

Benign

1.0

PrimateAI

Benign

0.23

PROVEAN

Benign

1.8

N;.

REVEL

Benign

0.021

Sift

Benign

1.0

T;.

Sift4G

Benign

1.0

T;.

Polyphen

0.0030

B;.

Vest4

0.017

ClinPred

0.0034

GERP RS

-2.0

Varity_R

0.052

gMVP

0.021

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.29

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.29

Position offset: -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