rs1042229

Variant names:

Your query was ambiguous. Multiple possible variants found:

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.576T>G(p.Asn192Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 1,613,830 control chromosomes in the GnomAD database, including 91,883 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. N192N) has been classified as Benign.

Frequency

Genomes: 𝑓 0.36 ( 10311 hom., cov: 31)

Exomes 𝑓: 0.33 ( 81572 hom. )

Consequence

FPR1
NM_002029.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.296

Publications

52 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=0.0011065602).

BP6

Variant 19-51746419-A-C is Benign according to our data. Variant chr19-51746419-A-C is described in ClinVar as [Benign]. Clinvar id is 402876.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FPR1	NM_002029.4 link	c.576T>G	p.Asn192Lys	missense_variant	Exon 2 of 2	ENST00000304748.5	NP_002020.1	P21462
FPR1	NM_001193306.2 link	c.576T>G	p.Asn192Lys	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.576T>G	p.Asn192Lys	missense_variant	Exon 2 of 2	1	NM_002029.4	ENSP00000302707.3	P21462
FPR1	ENST00000594900.2 link	c.576T>G	p.Asn192Lys	missense_variant	Exon 3 of 3	4		ENSP00000470750.2	P21462M0QZT0
FPR1	ENST00000595042.5 link	c.576T>G	p.Asn192Lys	missense_variant	Exon 3 of 3	2		ENSP00000471493.1	P21462
FPR1	ENST00000600815.2 link	c.576T>G	p.Asn192Lys	missense_variant	Exon 2 of 2	3		ENSP00000472936.2	P21462M0R315

Frequencies

GnomAD3 genomes

AF:

0.362

AC:

54938

AN:

151860

Hom.:

10298

Cov.:

show subpopulations

Gnomad AFR

AF:

0.461

Gnomad AMI

AF:

0.532

Gnomad AMR

AF:

0.301

Gnomad ASJ

AF:

0.352

Gnomad EAS

AF:

0.299

Gnomad SAS

AF:

0.319

Gnomad FIN

AF:

0.295

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.331

Gnomad OTH

AF:

0.376

GnomAD2 exomes

AF:

0.319

AC:

80159

AN:

251308

AF XY:

0.321

show subpopulations

Gnomad AFR exome

AF:

0.464

Gnomad AMR exome

AF:

0.223

Gnomad ASJ exome

AF:

0.345

Gnomad EAS exome

AF:

0.279

Gnomad FIN exome

AF:

0.293

Gnomad NFE exome

AF:

0.336

Gnomad OTH exome

AF:

0.336

GnomAD4 exome

AF:

0.331

AC:

484143

AN:

1461852

Hom.:

81572

Cov.:

AF XY:

0.331

AC XY:

241038

AN XY:

727238

show subpopulations

African (AFR)

AF:

0.472

AC:

15809

AN:

33480

American (AMR)

AF:

0.230

AC:

10295

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.345

AC:

9017

AN:

26136

East Asian (EAS)

AF:

0.329

AC:

13047

AN:

39700

South Asian (SAS)

AF:

0.318

AC:

27396

AN:

86258

European-Finnish (FIN)

AF:

0.293

AC:

15666

AN:

53412

Middle Eastern (MID)

AF:

0.434

AC:

2506

AN:

5768

European-Non Finnish (NFE)

AF:

0.332

AC:

369703

AN:

1111980

Other (OTH)

AF:

0.343

AC:

20704

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

22263

44527

66790

89054

111317

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.362

AC:

54982

AN:

151978

Hom.:

10311

Cov.:

AF XY:

0.359

AC XY:

26692

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.461

AC:

19096

AN:

41432

American (AMR)

AF:

0.301

AC:

4605

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.352

AC:

1221

AN:

3464

East Asian (EAS)

AF:

0.300

AC:

1539

AN:

5136

South Asian (SAS)

AF:

0.319

AC:

1535

AN:

4814

European-Finnish (FIN)

AF:

0.295

AC:

3118

AN:

10572

Middle Eastern (MID)

AF:

0.350

AC:

103

AN:

294

European-Non Finnish (NFE)

AF:

0.331

AC:

22496

AN:

67958

Other (OTH)

AF:

0.373

AC:

786

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1775

3550

5325

7100

8875

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.461

Hom.:

41618

TwinsUK

AF:

0.337

AC:

1248

ALSPAC

AF:

0.333

AC:

1282

ESP6500AA

AF:

0.506

AC:

2231

ESP6500EA

AF:

0.396

AC:

3403

ExAC

AF:

0.327

AC:

39638

EpiCase

AF:

0.350

EpiControl

AF:

0.348

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Oct 29, 2020

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is associated with the following publications: (PMID: 12595898) -

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: Frequency -

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

0.14

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.20

(source)

DANN

Benign

0.16

DEOGEN2

Benign

0.045

T;T

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.0013

LIST_S2

Benign

0.21

.;T

MetaRNN

Benign

0.0011

T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

-0.97

N;N

PhyloP100

0.30

PrimateAI

Benign

0.25

PROVEAN

Benign

1.4

.;N

REVEL

Benign

0.044

Sift

Benign

1.0

.;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0

B;B

Vest4

0.016

MutPred

0.32

Gain of methylation at N192 (P = 0.0076);Gain of methylation at N192 (P = 0.0076);

MPC

0.35

ClinPred

0.00026

GERP RS

1.5

Varity_R

0.034

gMVP

0.30

Mutation Taster

=99/1

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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rs1042229

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