NM_002029.4:c.301G>C

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002029.4(FPR1):c.301G>C(p.Val101Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 1,613,728 control chromosomes in the GnomAD database, including 114,578 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V101I) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.37 ( 10673 hom., cov: 31)

Exomes 𝑓: 0.37 ( 103905 hom. )

Consequence

FPR1
NM_002029.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3O:1

Conservation

PhyloP100: 0.283

Publications

49 publications found

Variant links:

Genes affected

FPR1 (HGNC:3826): (formyl peptide receptor 1) This gene encodes a G protein-coupled receptor of mammalian phagocytic cells that is a member of the G-protein coupled receptor 1 family. The protein mediates the response of phagocytic cells to invasion of the host by microorganisms and is important in host defense and inflammation.[provided by RefSeq, Jul 2010]

FPR1 Gene-Disease associations (from GenCC):

susceptibility to localized juvenile periodontitis
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Tourette syndrome
Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

FPR1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=7.5453434E-5).

BP6

Variant 19-51746694-C-G is Benign according to our data. Variant chr19-51746694-C-G is described in ClinVar as Benign. ClinVar VariationId is 402878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FPR1	NM_002029.4 link	c.301G>C	p.Val101Leu	missense_variant	Exon 2 of 2	ENST00000304748.5	NP_002020.1	P21462
FPR1	NM_001193306.2 link	c.301G>C	p.Val101Leu	missense_variant	Exon 3 of 3		NP_001180235.1	P21462

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
FPR1	ENST00000304748.5 link	c.301G>C	p.Val101Leu	missense_variant	Exon 2 of 2	1	NM_002029.4	ENSP00000302707.3	P21462
FPR1	ENST00000594900.2 link	c.301G>C	p.Val101Leu	missense_variant	Exon 3 of 3	4		ENSP00000470750.2	P21462M0QZT0
FPR1	ENST00000595042.5 link	c.301G>C	p.Val101Leu	missense_variant	Exon 3 of 3	2		ENSP00000471493.1	P21462
FPR1	ENST00000600815.2 link	c.301G>C	p.Val101Leu	missense_variant	Exon 2 of 2	3		ENSP00000472936.2	P21462M0R315

Frequencies

GnomAD3 genomes

AF:

0.370

AC:

56191

AN:

151790

Hom.:

10667

Cov.:

show subpopulations

Gnomad AFR

AF:

0.319

Gnomad AMI

AF:

0.176

Gnomad AMR

AF:

0.487

Gnomad ASJ

AF:

0.277

Gnomad EAS

AF:

0.483

Gnomad SAS

AF:

0.354

Gnomad FIN

AF:

0.441

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.365

Gnomad OTH

AF:

0.366

GnomAD2 exomes

AF:

0.401

AC:

100695

AN:

251342

AF XY:

0.390

show subpopulations

Gnomad AFR exome

AF:

0.317

Gnomad AMR exome

AF:

0.607

Gnomad ASJ exome

AF:

0.271

Gnomad EAS exome

AF:

0.476

Gnomad FIN exome

AF:

0.436

Gnomad NFE exome

AF:

0.358

Gnomad OTH exome

AF:

0.383

GnomAD4 exome

AF:

0.372

AC:

544174

AN:

1461820

Hom.:

103905

Cov.:

AF XY:

0.370

AC XY:

269277

AN XY:

727210

show subpopulations

African (AFR)

AF:

0.311

AC:

10415

AN:

33480

American (AMR)

AF:

0.593

AC:

26527

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.272

AC:

7108

AN:

26136

East Asian (EAS)

AF:

0.486

AC:

19282

AN:

39698

South Asian (SAS)

AF:

0.352

AC:

30333

AN:

86256

European-Finnish (FIN)

AF:

0.438

AC:

23422

AN:

53414

Middle Eastern (MID)

AF:

0.298

AC:

1720

AN:

5768

European-Non Finnish (NFE)

AF:

0.363

AC:

403140

AN:

1111952

Other (OTH)

AF:

0.368

AC:

22227

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

21950

43900

65850

87800

109750

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12986

25972

38958

51944

64930

<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:

0.370

AC:

56221

AN:

151908

Hom.:

10673

Cov.:

AF XY:

0.375

AC XY:

27859

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.319

AC:

13203

AN:

41404

American (AMR)

AF:

0.487

AC:

7435

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.277

AC:

959

AN:

3468

East Asian (EAS)

AF:

0.482

AC:

2486

AN:

5158

South Asian (SAS)

AF:

0.353

AC:

1703

AN:

4820

European-Finnish (FIN)

AF:

0.441

AC:

4659

AN:

10560

Middle Eastern (MID)

AF:

0.276

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.365

AC:

24769

AN:

67928

Other (OTH)

AF:

0.363

AC:

766

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1827

3655

5482

7310

9137

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

540

1080

1620

2160

2700

<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:

0.312

Hom.:

2306

Bravo

AF:

0.375

TwinsUK

AF:

0.365

AC:

1354

ALSPAC

AF:

0.362

AC:

1394

ESP6500AA

AF:

0.315

AC:

1389

ESP6500EA

AF:

0.358

AC:

3075

ExAC

AF:

0.389

AC:

47241

EpiCase

AF:

0.350

EpiControl

AF:

0.347

ClinVar

Significance: Benign

Submissions summary: Benign:3Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1Other:1

GenomeConnect, ClinGen

Significance:not provided

Review Status:no classification provided

Collection Method:phenotyping only

Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

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: MAF -

Gingival disorder

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.33

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.72

CADD

Benign

0.20

(source)

DANN

Benign

0.35

DEOGEN2

Benign

0.049

T;T;.

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.029

LIST_S2

Benign

0.064

.;T;T

MetaRNN

Benign

0.000075

T;T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

0.96

L;L;.

PhyloP100

0.28

PrimateAI

Benign

0.41

PROVEAN

Benign

-1.0

.;N;.

REVEL

Benign

0.052

Sift

Benign

0.24

.;T;.

Sift4G

Benign

0.65

T;T;.

Polyphen

0.0010

B;B;.

Vest4

0.019

MPC

0.30

ClinPred

0.0047

GERP RS

-2.0

Varity_R

0.084

gMVP

0.33

Mutation Taster

=100/0

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over