19-51746507-C-T

Variant names:

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_002029.4(FPR1):c.488G>A(p.Arg163His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00439 in 1,614,120 control chromosomes in the GnomAD database, including 26 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 (★★).

Frequency

Genomes: 𝑓 0.0058 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0042 ( 23 hom. )

Consequence

FPR1
NM_002029.4 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 2.92

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 -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0054709613).

BP6

Variant 19-51746507-C-T is Benign according to our data. Variant chr19-51746507-C-T is described in ClinVar as [Benign]. Clinvar id is 456367.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FPR1	NM_002029.4 link	c.488G>A	p.Arg163His	missense_variant	Exon 2 of 2	ENST00000304748.5	NP_002020.1	P21462
FPR1	NM_001193306.2 link	c.488G>A	p.Arg163His	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.488G>A	p.Arg163His	missense_variant	Exon 2 of 2	1	NM_002029.4	ENSP00000302707.3	P21462
FPR1	ENST00000594900.2 link	c.488G>A	p.Arg163His	missense_variant	Exon 3 of 3	4		ENSP00000470750.2	P21462M0QZT0
FPR1	ENST00000595042.5 link	c.488G>A	p.Arg163His	missense_variant	Exon 3 of 3	2		ENSP00000471493.1	P21462
FPR1	ENST00000600815.2 link	c.488G>A	p.Arg163His	missense_variant	Exon 2 of 2	3		ENSP00000472936.2	P21462M0R315

Frequencies

GnomAD3 genomes

AF:

0.00577

AC:

877

AN:

152114

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00928

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00557

Gnomad ASJ

AF:

0.0124

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.000829

Gnomad FIN

AF:

0.00170

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00473

Gnomad OTH

AF:

0.00718

GnomAD3 exomes

AF:

0.00414

AC:

1041

AN:

251308

Hom.:

AF XY:

0.00402

AC XY:

546

AN XY:

135816

show subpopulations

Gnomad AFR exome

AF:

0.00861

Gnomad AMR exome

AF:

0.00402

Gnomad ASJ exome

AF:

0.0105

Gnomad EAS exome

AF:

0.000435

Gnomad SAS exome

AF:

0.000849

Gnomad FIN exome

AF:

0.00143

Gnomad NFE exome

AF:

0.00490

Gnomad OTH exome

AF:

0.00554

GnomAD4 exome

AF:

0.00424

AC:

6201

AN:

1461888

Hom.:

Cov.:

AF XY:

0.00417

AC XY:

3030

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.0103

Gnomad4 AMR exome

AF:

0.00405

Gnomad4 ASJ exome

AF:

0.00979

Gnomad4 EAS exome

AF:

0.000202

Gnomad4 SAS exome

AF:

0.000939

Gnomad4 FIN exome

AF:

0.00139

Gnomad4 NFE exome

AF:

0.00444

Gnomad4 OTH exome

AF:

0.00474

GnomAD4 genome

AF:

0.00579

AC:

881

AN:

152232

Hom.:

Cov.:

AF XY:

0.00578

AC XY:

430

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.00937

Gnomad4 AMR

AF:

0.00556

Gnomad4 ASJ

AF:

0.0124

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.000830

Gnomad4 FIN

AF:

0.00170

Gnomad4 NFE

AF:

0.00473

Gnomad4 OTH

AF:

0.00710

Alfa

AF:

0.00560

Hom.:

Bravo

AF:

0.00646

TwinsUK

AF:

0.00593

AC:

ALSPAC

AF:

0.00467

AC:

ESP6500AA

AF:

0.00908

AC:

ESP6500EA

AF:

0.00395

AC:

ExAC

AF:

0.00382

AC:

464

Asia WGS

AF:

0.00289

AC:

AN:

3478

EpiCase

AF:

0.00545

EpiControl

AF:

0.00539

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Gingival disorder

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

FPR1-related disorder

Benign:1

Mar 17, 2020

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.25

BayesDel_addAF

Benign

-0.41

BayesDel_noAF

Benign

-0.36

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.039

T;T;.

Eigen

Benign

-0.55

Eigen_PC

Benign

-0.64

FATHMM_MKL

Benign

0.23

LIST_S2

Benign

0.59

.;T;T

M_CAP

Benign

0.023

MetaRNN

Benign

0.0055

T;T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

1.1

L;L;.

PrimateAI

Benign

0.25

PROVEAN

Benign

0.37

.;N;.

REVEL

Benign

0.12

Sift

Uncertain

0.021

.;D;.

Sift4G

Benign

0.14

T;T;.

Polyphen

0.68

P;P;.

Vest4

0.17

MVP

0.82

MPC

0.63

ClinPred

0.027

GERP RS

2.6

Varity_R

0.067

gMVP

0.40

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