Genetic Variant OR52M1:p.Phe14SerfsTer32 (chr11-4545229-CT-C) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2

The NM_001004137.1(OR52M1):c.41delT(p.Phe14SerfsTer32) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00406 in 1,612,378 control chromosomes in the GnomAD database, including 100 homozygotes. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0091 ( 12 hom., cov: 32)

Exomes 𝑓: 0.0035 ( 88 hom. )

Consequence

OR52M1
NM_001004137.1 frameshift

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.22

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 -9 ACMG points.

BP6

Variant 11-4545229-CT-C is Benign according to our data. Variant chr11-4545229-CT-C is described in ClinVar as [Benign]. Clinvar id is 3055530.Status of the report is no_assertion_criteria_provided, 0 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00906 (1380/152284) while in subpopulation EAS AF= 0.0445 (230/5168). AF 95% confidence interval is 0.0398. There are 12 homozygotes in gnomad4. There are 692 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 12 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR52M1	NM_001004137.1 link	c.41delT	p.Phe14SerfsTer32	frameshift_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.41delT	p.Phe14SerfsTer32	frameshift_variant	Exon 1 of 1	6	NM_001004137.1	ENSP00000353343.1		Q8NGK5

Frequencies

GnomAD3 genomes

AF:

0.00902

AC:

1373

AN:

152168

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0217

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00524

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0444

Gnomad SAS

AF:

0.0212

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000573

Gnomad OTH

AF:

0.0105

GnomAD3 exomes

AF:

0.00793

AC:

1975

AN:

248920

Hom.:

AF XY:

0.00814

AC XY:

1095

AN XY:

134468

show subpopulations

Gnomad AFR exome

AF:

0.0225

Gnomad AMR exome

AF:

0.00221

Gnomad ASJ exome

AF:

0.000203

Gnomad EAS exome

AF:

0.0478

Gnomad SAS exome

AF:

0.0181

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000668

Gnomad OTH exome

AF:

0.00511

GnomAD4 exome

AF:

0.00354

AC:

5162

AN:

1460094

Hom.:

Cov.:

AF XY:

0.00400

AC XY:

2909

AN XY:

726346

show subpopulations

Gnomad4 AFR exome

AF:

0.0230

Gnomad4 AMR exome

AF:

0.00251

Gnomad4 ASJ exome

AF:

0.000193

Gnomad4 EAS exome

AF:

0.0361

Gnomad4 SAS exome

AF:

0.0186

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000671

Gnomad4 OTH exome

AF:

0.00767

GnomAD4 genome

AF:

0.00906

AC:

1380

AN:

152284

Hom.:

Cov.:

AF XY:

0.00929

AC XY:

692

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.0218

Gnomad4 AMR

AF:

0.00523

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0445

Gnomad4 SAS

AF:

0.0214

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000573

Gnomad4 OTH

AF:

0.0104

Alfa

AF:

0.00128

Hom.:

Bravo

AF:

0.00976

Asia WGS

AF:

0.0330

AC:

115

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

OR52M1-related disorder

Benign:1

Jun 10, 2020

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

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