Variant chr15-22094753-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The NM_001005241.4(OR4N4):c.232G>C(p.Ala78Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0019 ( 0 hom., cov: 0)

Exomes 𝑓: 0.56 ( 8031 hom. )

Failed GnomAD Quality Control

Consequence

OR4N4
NM_001005241.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.375

Variant links:

Genes affected

OR4N4 (HGNC:15375): (olfactory receptor family 4 subfamily N 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]

OR4N4 links:

OR4M2-OT1 (HGNC:):

OR4M2-OT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0021137595).

BP6

Variant 15-22094753-G-C is Benign according to our data. Variant chr15-22094753-G-C is described in ClinVar as [Benign]. Clinvar id is 769405.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
OR4N4	NM_001005241.4 linkuse as main transcript	c.232G>C	p.Ala78Pro	missense_variant	1/1	ENST00000328795.6
OR4M2-OT1	NR_110480.1 linkuse as main transcript	n.1064G>C		non_coding_transcript_exon_variant	8/9
OR4M2-OT1	NR_110481.1 linkuse as main transcript	n.796G>C		non_coding_transcript_exon_variant	6/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR4N4	ENST00000328795.6 linkuse as main transcript	c.232G>C	p.Ala78Pro	missense_variant	1/1		NM_001005241.4	P1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

1070

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad EAS

AF:

0.500

Gnomad SAS

AF:

0.500

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.188

AC:

44376

AN:

236452

Hom.:

859

AF XY:

0.194

AC XY:

24768

AN XY:

127404

show subpopulations

Gnomad AFR exome

AF:

0.0382

Gnomad AMR exome

AF:

0.103

Gnomad ASJ exome

AF:

0.236

Gnomad EAS exome

AF:

0.177

Gnomad SAS exome

AF:

0.232

Gnomad FIN exome

AF:

0.206

Gnomad NFE exome

AF:

0.218

Gnomad OTH exome

AF:

0.211

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.562

AC:

24113

AN:

42928

Hom.:

8031

Cov.:

AF XY:

0.572

AC XY:

12467

AN XY:

21812

show subpopulations

Gnomad4 AFR exome

AF:

0.0683

Gnomad4 AMR exome

AF:

0.473

Gnomad4 ASJ exome

AF:

0.690

Gnomad4 EAS exome

AF:

0.346

Gnomad4 SAS exome

AF:

0.599

Gnomad4 FIN exome

AF:

0.766

Gnomad4 NFE exome

AF:

0.682

Gnomad4 OTH exome

AF:

0.524

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00187

AC:

AN:

1068

Hom.:

Cov.:

AF XY:

0.00413

AC XY:

AN XY:

484

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.500

Gnomad4 SAS

AF:

0.500

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.418

Hom.:

3239

ESP6500AA

AF:

0.0352

AC:

155

ESP6500EA

AF:

0.163

AC:

1405

ExAC

AF:

0.200

AC:

24209

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jun 23, 2017	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.017

.;T

Eigen

Benign

-0.56

Eigen_PC

Benign

-0.64

FATHMM_MKL

Benign

0.12

LIST_S2

Benign

0.20

T;.

MetaRNN

Benign

0.0021

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.1

.;M

MutationTaster

Benign

0.89

PrimateAI

Benign

0.35

PROVEAN

Uncertain

-2.5

.;N

REVEL

Benign

0.11

Sift

Benign

0.045

.;D

Sift4G

Benign

0.063

.;T

Polyphen

0.0050

.;B

Vest4

0.13

MPC

0.36

ClinPred

0.010

GERP RS

2.3

Varity_R

0.72

gMVP

0.37

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over