Genetic Variant NM_001004137.1:c.291C>T (chr11-4545481-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001004137.1(OR52M1):c.291C>T(p.Asp97Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 1,613,842 control chromosomes in the GnomAD database, including 198,636 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.49 ( 18262 hom., cov: 32)

Exomes 𝑓: 0.49 ( 180374 hom. )

Consequence

OR52M1
NM_001004137.1 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.656

Variant links:

Genes affected

OR52M1 (HGNC:15225): (olfactory receptor family 52 subfamily M 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]

OR52M1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 11-4545481-C-T is Benign according to our data. Variant chr11-4545481-C-T is described in ClinVar as [Benign]. Clinvar id is 3060906.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.656 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR52M1	NM_001004137.1 link	c.291C>T	p.Asp97Asp	synonymous_variant	Exon 1 of 1	ENST00000360213.1	NP_001004137.1	Q8NGK5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR52M1	ENST00000360213.1 link	c.291C>T	p.Asp97Asp	synonymous_variant	Exon 1 of 1	6	NM_001004137.1	ENSP00000353343.1		Q8NGK5

Frequencies

GnomAD3 genomes

AF:

0.486

AC:

73868

AN:

151974

Hom.:

18253

Cov.:

show subpopulations

Gnomad AFR

AF:

0.505

Gnomad AMI

AF:

0.541

Gnomad AMR

AF:

0.374

Gnomad ASJ

AF:

0.616

Gnomad EAS

AF:

0.294

Gnomad SAS

AF:

0.502

Gnomad FIN

AF:

0.469

Gnomad MID

AF:

0.472

Gnomad NFE

AF:

0.508

Gnomad OTH

AF:

0.500

GnomAD3 exomes

AF:

0.451

AC:

113179

AN:

251038

Hom.:

26931

AF XY:

0.462

AC XY:

62665

AN XY:

135664

show subpopulations

Gnomad AFR exome

AF:

0.508

Gnomad AMR exome

AF:

0.253

Gnomad ASJ exome

AF:

0.612

Gnomad EAS exome

AF:

0.282

Gnomad SAS exome

AF:

0.496

Gnomad FIN exome

AF:

0.454

Gnomad NFE exome

AF:

0.502

Gnomad OTH exome

AF:

0.472

GnomAD4 exome

AF:

0.493

AC:

720375

AN:

1461750

Hom.:

180374

Cov.:

AF XY:

0.494

AC XY:

358887

AN XY:

727156

show subpopulations

Gnomad4 AFR exome

AF:

0.508

Gnomad4 AMR exome

AF:

0.268

Gnomad4 ASJ exome

AF:

0.607

Gnomad4 EAS exome

AF:

0.302

Gnomad4 SAS exome

AF:

0.491

Gnomad4 FIN exome

AF:

0.458

Gnomad4 NFE exome

AF:

0.507

Gnomad4 OTH exome

AF:

0.493

GnomAD4 genome

AF:

0.486

AC:

73918

AN:

152092

Hom.:

18262

Cov.:

AF XY:

0.481

AC XY:

35755

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.505

Gnomad4 AMR

AF:

0.373

Gnomad4 ASJ

AF:

0.616

Gnomad4 EAS

AF:

0.295

Gnomad4 SAS

AF:

0.502

Gnomad4 FIN

AF:

0.469

Gnomad4 NFE

AF:

0.508

Gnomad4 OTH

AF:

0.500

Alfa

AF:

0.493

Hom.:

20657

Bravo

AF:

0.478

Asia WGS

AF:

0.401

AC:

1394

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

OR52M1-related disorder

Benign:1

Jul 11, 2023

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

2.3

DANN

Benign

0.40

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