19-51746963-A-G

Position:

chr19-51746963-A-G

Variant summary

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

The ENST00000304748.5(FPR1):c.32T>C(p.Ile11Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 1,613,220 control chromosomes in the GnomAD database, including 496,799 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.79 ( 47477 hom., cov: 29)

Exomes 𝑓: 0.78 ( 449322 hom. )

Consequence

FPR1
ENST00000304748.5 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.885

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=7.877735E-7).

BP6

Variant 19-51746963-A-G is Benign according to our data. Variant chr19-51746963-A-G is described in ClinVar as [Benign]. Clinvar id is 402879.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 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.32T>C	p.Ile11Thr	missense_variant	2/2	ENST00000304748.5	NP_002020.1
FPR1	NM_001193306.2 linkuse as main transcript	c.32T>C	p.Ile11Thr	missense_variant	3/3		NP_001180235.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
FPR1	ENST00000304748.5 linkuse as main transcript	c.32T>C	p.Ile11Thr	missense_variant	2/2	1	NM_002029.4	ENSP00000302707	P1
FPR1	ENST00000594900.2 linkuse as main transcript	c.32T>C	p.Ile11Thr	missense_variant	3/3	4		ENSP00000470750	P1
FPR1	ENST00000595042.5 linkuse as main transcript	c.32T>C	p.Ile11Thr	missense_variant	3/3	2		ENSP00000471493	P1
FPR1	ENST00000600815.2 linkuse as main transcript	c.32T>C	p.Ile11Thr	missense_variant	2/2	3		ENSP00000472936	P1

Frequencies

GnomAD3 genomes

AF:

0.790

AC:

119956

AN:

151872

Hom.:

47444

Cov.:

show subpopulations

Gnomad AFR

AF:

0.788

Gnomad AMI

AF:

0.867

Gnomad AMR

AF:

0.797

Gnomad ASJ

AF:

0.804

Gnomad EAS

AF:

0.964

Gnomad SAS

AF:

0.869

Gnomad FIN

AF:

0.797

Gnomad MID

AF:

0.788

Gnomad NFE

AF:

0.767

Gnomad OTH

AF:

0.792

GnomAD3 exomes

AF:

0.807

AC:

202193

AN:

250618

Hom.:

81836

AF XY:

0.806

AC XY:

109167

AN XY:

135434

show subpopulations

Gnomad AFR exome

AF:

0.794

Gnomad AMR exome

AF:

0.827

Gnomad ASJ exome

AF:

0.810

Gnomad EAS exome

AF:

0.960

Gnomad SAS exome

AF:

0.854

Gnomad FIN exome

AF:

0.800

Gnomad NFE exome

AF:

0.767

Gnomad OTH exome

AF:

0.785

GnomAD4 exome

AF:

0.783

AC:

1144305

AN:

1461230

Hom.:

449322

Cov.:

AF XY:

0.785

AC XY:

570490

AN XY:

726900

show subpopulations

Gnomad4 AFR exome

AF:

0.791

Gnomad4 AMR exome

AF:

0.822

Gnomad4 ASJ exome

AF:

0.810

Gnomad4 EAS exome

AF:

0.970

Gnomad4 SAS exome

AF:

0.854

Gnomad4 FIN exome

AF:

0.803

Gnomad4 NFE exome

AF:

0.768

Gnomad4 OTH exome

AF:

0.785

GnomAD4 genome

AF:

0.790

AC:

120039

AN:

151990

Hom.:

47477

Cov.:

AF XY:

0.793

AC XY:

58945

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.788

Gnomad4 AMR

AF:

0.797

Gnomad4 ASJ

AF:

0.804

Gnomad4 EAS

AF:

0.964

Gnomad4 SAS

AF:

0.869

Gnomad4 FIN

AF:

0.797

Gnomad4 NFE

AF:

0.767

Gnomad4 OTH

AF:

0.786

Alfa

AF:

0.775

Hom.:

100648

Bravo

AF:

0.789

TwinsUK

AF:

0.771

AC:

2858

ALSPAC

AF:

0.774

AC:

2983

ESP6500AA

AF:

0.792

AC:

3488

ESP6500EA

AF:

0.763

AC:

6559

ExAC

AF:

0.804

AC:

97618

Asia WGS

AF:

0.851

AC:

2959

AN:

3478

EpiCase

AF:

0.764

EpiControl

AF:

0.769

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

0.12

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.0050

DANN

Benign

0.49

DEOGEN2

Benign

0.066

T;T;.;.

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.00082

LIST_S2

Benign

0.23

.;T;T;T

MetaRNN

Benign

7.9e-7

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.34

N;N;.;.

MutationTaster

Benign

1.0

PrimateAI

Benign

0.26

PROVEAN

Benign

0.21

.;N;.;.

REVEL

Benign

0.030

Sift

Benign

0.63

.;T;.;.

Sift4G

Benign

0.77

T;T;.;.

Polyphen

0.0080

B;B;.;.

Vest4

0.010

MPC

0.38

ClinPred

0.0061

GERP RS

-6.9

Varity_R

0.041

gMVP

0.097

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