rs34672924

Variant names:

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001004752.2(OR51F1):c.295delC(p.Arg99ValfsTer41) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 1,603,756 control chromosomes in the GnomAD database, including 49,713 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.28 ( 6945 hom., cov: 20)

Exomes 𝑓: 0.23 ( 42768 hom. )

Consequence

OR51F1
NM_001004752.2 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.839

Publications

13 publications found

Variant links:

Genes affected

OR51F1 (HGNC:15196): (olfactory receptor family 51 subfamily F 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. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional. [provided by RefSeq, Jun 2015]

OR51F1 links:

MMP26 (HGNC:14249): (matrix metallopeptidase 26) Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. The encoded preproprotein is proteolytically processed to generate the mature enzyme. This enzyme may degrade collagen type IV, fibronectin, fibrinogen, and beta-casein, and activate matrix metalloproteinase-9 by cleavage. The protein differs from most MMP family members in that it lacks a conserved C-terminal protein domain. The encoded protein may promote cell invasion in multiple human cancers. [provided by RefSeq, May 2016]

MMP26 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 11-4769643-CG-C is Benign according to our data. Variant chr11-4769643-CG-C is described in ClinVar as Benign. ClinVar VariationId is 403275.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004752.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
OR51F1	NM_001004752.2	MANE Select	c.295delC	p.Arg99ValfsTer41	frameshift	Exon 1 of 1	NP_001004752.2	A6NGY5
MMP26	NM_021801.5	MANE Select	c.-145+2303delG		intron	N/A	NP_068573.2	Q9NRE1
MMP26	NM_001384608.1		c.-153+2303delG		intron	N/A	NP_001371537.1	A0A8J8YUH5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
OR51F1	ENST00000624103.2	TSL:6 MANE Select	c.295delC	p.Arg99ValfsTer41	frameshift	Exon 1 of 1	ENSP00000485387.2	A6NGY5
MMP26	ENST00000380390.6	TSL:5 MANE Select	c.-145+2303delG		intron	N/A	ENSP00000369753.1	Q9NRE1
MMP26	ENST00000300762.2	TSL:1	c.-153+2303delG		intron	N/A	ENSP00000300762.2	A0A8J8YUH5

Frequencies

GnomAD3 genomes

AF:

0.280

AC:

42465

AN:

151834

Hom.:

6933

Cov.:

show subpopulations

Gnomad AFR

AF:

0.436

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.228

Gnomad ASJ

AF:

0.356

Gnomad EAS

AF:

0.000772

Gnomad SAS

AF:

0.0986

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.312

Gnomad NFE

AF:

0.245

Gnomad OTH

AF:

0.301

GnomAD2 exomes

AF:

0.207

AC:

51645

AN:

249938

AF XY:

0.203

show subpopulations

Gnomad AFR exome

AF:

0.436

Gnomad AMR exome

AF:

0.146

Gnomad ASJ exome

AF:

0.348

Gnomad EAS exome

AF:

0.000326

Gnomad FIN exome

AF:

0.169

Gnomad NFE exome

AF:

0.248

Gnomad OTH exome

AF:

0.235

GnomAD4 exome

AF:

0.230

AC:

333584

AN:

1451804

Hom.:

42768

Cov.:

AF XY:

0.226

AC XY:

163425

AN XY:

722640

show subpopulations

African (AFR)

AF:

0.450

AC:

14903

AN:

33130

American (AMR)

AF:

0.156

AC:

6981

AN:

44684

Ashkenazi Jewish (ASJ)

AF:

0.345

AC:

8976

AN:

26032

East Asian (EAS)

AF:

0.000327

AC:

AN:

39700

South Asian (SAS)

AF:

0.100

AC:

8651

AN:

86088

European-Finnish (FIN)

AF:

0.173

AC:

9225

AN:

53382

Middle Eastern (MID)

AF:

0.296

AC:

1704

AN:

5748

European-Non Finnish (NFE)

AF:

0.243

AC:

268509

AN:

1102940

Other (OTH)

AF:

0.243

AC:

14622

AN:

60100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.413

Heterozygous variant carriers

12769

25538

38307

51076

63845

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8936

17872

26808

35744

44680

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.280

AC:

42524

AN:

151952

Hom.:

6945

Cov.:

AF XY:

0.269

AC XY:

19971

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.436

AC:

18046

AN:

41376

American (AMR)

AF:

0.227

AC:

3472

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.356

AC:

1234

AN:

3464

East Asian (EAS)

AF:

0.000967

AC:

AN:

5168

South Asian (SAS)

AF:

0.0987

AC:

476

AN:

4822

European-Finnish (FIN)

AF:

0.164

AC:

1738

AN:

10586

Middle Eastern (MID)

AF:

0.312

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.245

AC:

16634

AN:

67944

Other (OTH)

AF:

0.298

AC:

629

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1478

2956

4434

5912

7390

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

406

812

1218

1624

2030

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.167

Hom.:

488

Bravo

AF:

0.299

Asia WGS

AF:

0.0760

AC:

266

AN:

3478

EpiCase

AF:

0.270

EpiControl

AF:

0.278

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.84

Mutation Taster

=190/10

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over