Variant chr1-248324336-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001004691.1(OR2M7):c.233T>C(p.Val78Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 1,613,894 control chromosomes in the GnomAD database, including 456,755 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.77 ( 44847 hom., cov: 31)

Exomes 𝑓: 0.75 ( 411908 hom. )

Consequence

OR2M7
NM_001004691.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.396

Variant links:

Genes affected

OR2M7 (HGNC:19594): (olfactory receptor family 2 subfamily M member 7) 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]

OR2M7 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=2.5854079E-6).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR2M7	NM_001004691.1 linkuse as main transcript	c.233T>C	p.Val78Ala	missense_variant	1/1	ENST00000317965.3	NP_001004691.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR2M7	ENST00000317965.3 linkuse as main transcript	c.233T>C	p.Val78Ala	missense_variant	1/1		NM_001004691.1	ENSP00000324557	P1

Frequencies

GnomAD3 genomes

AF:

0.766

AC:

116407

AN:

151974

Hom.:

44816

Cov.:

show subpopulations

Gnomad AFR

AF:

0.780

Gnomad AMI

AF:

0.855

Gnomad AMR

AF:

0.777

Gnomad ASJ

AF:

0.700

Gnomad EAS

AF:

0.859

Gnomad SAS

AF:

0.875

Gnomad FIN

AF:

0.802

Gnomad MID

AF:

0.737

Gnomad NFE

AF:

0.738

Gnomad OTH

AF:

0.750

GnomAD3 exomes

AF:

0.774

AC:

194513

AN:

251346

Hom.:

75602

AF XY:

0.777

AC XY:

105608

AN XY:

135834

show subpopulations

Gnomad AFR exome

AF:

0.775

Gnomad AMR exome

AF:

0.772

Gnomad ASJ exome

AF:

0.705

Gnomad EAS exome

AF:

0.864

Gnomad SAS exome

AF:

0.859

Gnomad FIN exome

AF:

0.799

Gnomad NFE exome

AF:

0.739

Gnomad OTH exome

AF:

0.755

GnomAD4 exome

AF:

0.750

AC:

1095897

AN:

1461802

Hom.:

411908

Cov.:

AF XY:

0.753

AC XY:

547504

AN XY:

727202

show subpopulations

Gnomad4 AFR exome

AF:

0.777

Gnomad4 AMR exome

AF:

0.771

Gnomad4 ASJ exome

AF:

0.702

Gnomad4 EAS exome

AF:

0.845

Gnomad4 SAS exome

AF:

0.860

Gnomad4 FIN exome

AF:

0.801

Gnomad4 NFE exome

AF:

0.734

Gnomad4 OTH exome

AF:

0.758

GnomAD4 genome

AF:

0.766

AC:

116493

AN:

152092

Hom.:

44847

Cov.:

AF XY:

0.771

AC XY:

57344

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.780

Gnomad4 AMR

AF:

0.777

Gnomad4 ASJ

AF:

0.700

Gnomad4 EAS

AF:

0.859

Gnomad4 SAS

AF:

0.874

Gnomad4 FIN

AF:

0.802

Gnomad4 NFE

AF:

0.738

Gnomad4 OTH

AF:

0.749

Alfa

AF:

0.740

Hom.:

61086

Bravo

AF:

0.762

TwinsUK

AF:

0.727

AC:

2694

ALSPAC

AF:

0.741

AC:

2854

ESP6500AA

AF:

0.776

AC:

3420

ESP6500EA

AF:

0.747

AC:

6420

ExAC

AF:

0.776

AC:

94168

Asia WGS

AF:

0.855

AC:

2969

AN:

3478

EpiCase

AF:

0.731

EpiControl

AF:

0.738

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.27

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.68

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0044

Eigen

Benign

-0.26

Eigen_PC

Benign

-0.48

FATHMM_MKL

Benign

0.049

LIST_S2

Benign

0.54

MetaRNN

Benign

0.0000026

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.2

MutationTaster

Benign

1.0

PrimateAI

Benign

0.28

PROVEAN

Uncertain

-3.8

REVEL

Benign

0.038

Sift

Uncertain

0.0030

Sift4G

Uncertain

0.024

Polyphen

0.97

Vest4

0.015

MPC

0.12

ClinPred

0.034

GERP RS

-0.011

Varity_R

0.34

gMVP

0.24

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