chr11-4769643-CG-C

Variant names:

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR51F1	NM_001004752.2 link	c.295delC	p.Arg99ValfsTer41	frameshift_variant	Exon 1 of 1	ENST00000624103.2	NP_001004752.2	A6NLW9
MMP26	NM_021801.5 link	c.-145+2303delG		intron_variant	Intron 2 of 7	ENST00000380390.6	NP_068573.2	Q9NRE1
MMP26	NM_001384608.1 link	c.-153+2303delG		intron_variant	Intron 2 of 7		NP_001371537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
OR51F1	ENST00000624103.2 link	c.295delC	p.Arg99ValfsTer41	frameshift_variant	Exon 1 of 1	6	NM_001004752.2	ENSP00000485387.2	A6NGY5A6NLW9
MMP26	ENST00000380390.6 link	c.-145+2303delG		intron_variant	Intron 2 of 7	5	NM_021801.5	ENSP00000369753.1	Q9NRE1
MMP26	ENST00000300762.2 link	c.-153+2303delG		intron_variant	Intron 2 of 7	1		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

GnomAD3 exomes

AF:

0.207

AC:

51645

AN:

249938

Hom.:

6810

AF XY:

0.203

AC XY:

27478

AN XY:

135060

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 SAS exome

AF:

0.0983

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

Gnomad4 AFR exome

AF:

0.450

Gnomad4 AMR exome

AF:

0.156

Gnomad4 ASJ exome

AF:

0.345

Gnomad4 EAS exome

AF:

0.000327

Gnomad4 SAS exome

AF:

0.100

Gnomad4 FIN exome

AF:

0.173

Gnomad4 NFE exome

AF:

0.243

Gnomad4 OTH exome

AF:

0.243

GnomAD4 genome

AF:

0.280

AC:

42524

AN:

151952

Hom.:

6945

Cov.:

AF XY:

0.269

AC XY:

19971

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.436

Gnomad4 AMR

AF:

0.227

Gnomad4 ASJ

AF:

0.356

Gnomad4 EAS

AF:

0.000967

Gnomad4 SAS

AF:

0.0987

Gnomad4 FIN

AF:

0.164

Gnomad4 NFE

AF:

0.245

Gnomad4 OTH

AF:

0.298

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

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in ESP (all): 4000/12518=31.95% -

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