rs5030880

Positions:

chr19-51746427-T-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002029.4(FPR1):c.568A>T(p.Arg190Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 1,613,846 control chromosomes in the GnomAD database, including 14,182 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1176 hom., cov: 31)

Exomes 𝑓: 0.13 ( 13006 hom. )

Consequence

FPR1
NM_002029.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4O:1

Conservation

PhyloP100: -0.104

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0026525855).

BP6

Variant 19-51746427-T-A is Benign according to our data. Variant chr19-51746427-T-A is described in ClinVar as [Benign]. Clinvar id is 834692.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FPR1	NM_002029.4 linkuse as main transcript	c.568A>T	p.Arg190Trp	missense_variant	2/2	ENST00000304748.5	NP_002020.1	P21462
FPR1	NM_001193306.2 linkuse as main transcript	c.568A>T	p.Arg190Trp	missense_variant	3/3		NP_001180235.1	P21462

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
FPR1	ENST00000304748.5 linkuse as main transcript	c.568A>T	p.Arg190Trp	missense_variant	2/2	1	NM_002029.4	ENSP00000302707.3	P21462
FPR1	ENST00000594900.2 linkuse as main transcript	c.568A>T	p.Arg190Trp	missense_variant	3/3	4		ENSP00000470750.2	P21462M0QZT0
FPR1	ENST00000595042.5 linkuse as main transcript	c.568A>T	p.Arg190Trp	missense_variant	3/3	2		ENSP00000471493.1	P21462
FPR1	ENST00000600815.2 linkuse as main transcript	c.568A>T	p.Arg190Trp	missense_variant	2/2	3		ENSP00000472936.2	P21462M0R315

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18393

AN:

151874

Hom.:

1173

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0880

Gnomad AMI

AF:

0.194

Gnomad AMR

AF:

0.0995

Gnomad ASJ

AF:

0.120

Gnomad EAS

AF:

0.200

Gnomad SAS

AF:

0.179

Gnomad FIN

AF:

0.172

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.127

Gnomad OTH

AF:

0.123

GnomAD3 exomes

AF:

0.133

AC:

33346

AN:

251326

Hom.:

2505

AF XY:

0.136

AC XY:

18523

AN XY:

135818

show subpopulations

Gnomad AFR exome

AF:

0.0839

Gnomad AMR exome

AF:

0.0851

Gnomad ASJ exome

AF:

0.118

Gnomad EAS exome

AF:

0.196

Gnomad SAS exome

AF:

0.186

Gnomad FIN exome

AF:

0.158

Gnomad NFE exome

AF:

0.126

Gnomad OTH exome

AF:

0.126

GnomAD4 exome

AF:

0.130

AC:

189986

AN:

1461854

Hom.:

13006

Cov.:

AF XY:

0.131

AC XY:

95476

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.0851

Gnomad4 AMR exome

AF:

0.0876

Gnomad4 ASJ exome

AF:

0.119

Gnomad4 EAS exome

AF:

0.160

Gnomad4 SAS exome

AF:

0.184

Gnomad4 FIN exome

AF:

0.165

Gnomad4 NFE exome

AF:

0.126

Gnomad4 OTH exome

AF:

0.134

GnomAD4 genome

AF:

0.121

AC:

18409

AN:

151992

Hom.:

1176

Cov.:

AF XY:

0.125

AC XY:

9285

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.0881

Gnomad4 AMR

AF:

0.0994

Gnomad4 ASJ

AF:

0.120

Gnomad4 EAS

AF:

0.199

Gnomad4 SAS

AF:

0.180

Gnomad4 FIN

AF:

0.172

Gnomad4 NFE

AF:

0.127

Gnomad4 OTH

AF:

0.127

Alfa

AF:

0.125

Hom.:

421

Bravo

AF:

0.111

TwinsUK

AF:

0.121

AC:

447

ALSPAC

AF:

0.124

AC:

477

ESP6500AA

AF:

0.0844

AC:

372

ESP6500EA

AF:

0.128

AC:

1098

ExAC

AF:

0.135

AC:

16337

Asia WGS

AF:

0.176

AC:

609

AN:

3478

EpiCase

AF:

0.123

EpiControl

AF:

0.124

ClinVar

Significance: Benign

Submissions summary: Benign:4Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2Other:1

Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 29, 2020	This variant is associated with the following publications: (PMID: 12595898) -
not provided, no classification provided	phenotyping only	GenomeConnect, ClinGen	-	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. -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

FPR1 POLYMORPHISM

Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Jan 07, 2025

- -

Gingival disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.36

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.081

T;T;.

Eigen

Benign

-0.72

Eigen_PC

Benign

-0.74

FATHMM_MKL

Benign

0.15

LIST_S2

Benign

0.51

.;T;T

MetaRNN

Benign

0.0027

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.95

L;L;.

PrimateAI

Benign

0.25

PROVEAN

Benign

-2.0

.;N;.

REVEL

Benign

0.031

Sift

Uncertain

0.027

.;D;.

Sift4G

Uncertain

0.023

D;D;.

Polyphen

0.0020

B;B;.

Vest4

0.044

MPC

0.32

ClinPred

0.014

GERP RS

2.6

Varity_R

0.074

gMVP

0.63

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