19-51745958-T-G

Position:

chr19-51745958-T-G

Variant summary

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

The NM_002029.4(FPR1):c.1037A>C(p.Glu346Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 1,609,306 control chromosomes in the GnomAD database, including 517,360 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 0.80 ( 48125 hom., cov: 30)

Exomes 𝑓: 0.80 ( 469235 hom. )

Consequence

FPR1
NM_002029.4 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.10

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=1.0961179E-6).

BP6

Variant 19-51745958-T-G is Benign according to our data. Variant chr19-51745958-T-G is described in ClinVar as [Benign]. Clinvar id is 402874.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.822 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.1037A>C	p.Glu346Ala	missense_variant	2/2	ENST00000304748.5	NP_002020.1	P21462
FPR1	NM_001193306.2 linkuse as main transcript	c.1037A>C	p.Glu346Ala	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.1037A>C	p.Glu346Ala	missense_variant	2/2	1	NM_002029.4	ENSP00000302707.3	P21462
FPR1	ENST00000594900.2 linkuse as main transcript	c.1037A>C	p.Glu346Ala	missense_variant	3/3	4		ENSP00000470750.2	P21462M0QZT0
FPR1	ENST00000595042.5 linkuse as main transcript	c.1037A>C	p.Glu346Ala	missense_variant	3/3	2		ENSP00000471493.1	P21462
FPR1	ENST00000600815.2 linkuse as main transcript	c.1037A>C	p.Glu346Ala	missense_variant	2/2	3		ENSP00000472936.2	P21462M0R315

Frequencies

GnomAD3 genomes

AF:

0.796

AC:

120916

AN:

151898

Hom.:

48097

Cov.:

show subpopulations

Gnomad AFR

AF:

0.790

Gnomad AMI

AF:

0.878

Gnomad AMR

AF:

0.810

Gnomad ASJ

AF:

0.791

Gnomad EAS

AF:

0.717

Gnomad SAS

AF:

0.844

Gnomad FIN

AF:

0.777

Gnomad MID

AF:

0.851

Gnomad NFE

AF:

0.801

Gnomad OTH

AF:

0.785

GnomAD3 exomes

AF:

0.803

AC:

201532

AN:

251018

Hom.:

81116

AF XY:

0.804

AC XY:

109087

AN XY:

135628

show subpopulations

Gnomad AFR exome

AF:

0.791

Gnomad AMR exome

AF:

0.851

Gnomad ASJ exome

AF:

0.785

Gnomad EAS exome

AF:

0.705

Gnomad SAS exome

AF:

0.848

Gnomad FIN exome

AF:

0.773

Gnomad NFE exome

AF:

0.801

Gnomad OTH exome

AF:

0.801

GnomAD4 exome

AF:

0.802

AC:

1168580

AN:

1457290

Hom.:

469235

Cov.:

AF XY:

0.804

AC XY:

581712

AN XY:

723872

show subpopulations

Gnomad4 AFR exome

AF:

0.794

Gnomad4 AMR exome

AF:

0.847

Gnomad4 ASJ exome

AF:

0.789

Gnomad4 EAS exome

AF:

0.721

Gnomad4 SAS exome

AF:

0.852

Gnomad4 FIN exome

AF:

0.782

Gnomad4 NFE exome

AF:

0.801

Gnomad4 OTH exome

AF:

0.798

GnomAD4 genome

AF:

0.796

AC:

120992

AN:

152016

Hom.:

48125

Cov.:

AF XY:

0.796

AC XY:

59098

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.790

Gnomad4 AMR

AF:

0.810

Gnomad4 ASJ

AF:

0.791

Gnomad4 EAS

AF:

0.717

Gnomad4 SAS

AF:

0.844

Gnomad4 FIN

AF:

0.777

Gnomad4 NFE

AF:

0.801

Gnomad4 OTH

AF:

0.780

Alfa

AF:

0.799

Hom.:

82562

Bravo

AF:

0.798

TwinsUK

AF:

0.799

AC:

2961

ALSPAC

AF:

0.799

AC:

3078

ESP6500AA

AF:

0.793

AC:

3495

ESP6500EA

AF:

0.799

AC:

6870

ExAC

AF:

0.804

AC:

97639

Asia WGS

AF:

0.721

AC:

2507

AN:

3478

EpiCase

AF:

0.801

EpiControl

AF:

0.797

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

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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. -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

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

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.082

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Benign

0.96

DEOGEN2

Benign

0.23

T;T

Eigen

Benign

-0.40

Eigen_PC

Benign

-0.58

FATHMM_MKL

Benign

0.038

LIST_S2

Benign

0.28

.;T

MetaRNN

Benign

0.0000011

T;T

MetaSVM

Benign

-0.91

MutationAssessor

Uncertain

2.7

M;M

MutationTaster

Benign

1.0

PrimateAI

Benign

0.36

PROVEAN

Uncertain

-3.5

.;D

REVEL

Benign

0.15

Sift

Benign

0.069

.;T

Sift4G

Uncertain

0.014

D;D

Polyphen

0.65

P;P

Vest4

0.066

MPC

0.34

ClinPred

0.033

GERP RS

3.1

Varity_R

0.14

gMVP

0.18

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