rs2070745

Positions:

Variant summary

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

The NM_002029.4(FPR1):c.301G>C(p.Val101Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 1,613,728 control chromosomes in the GnomAD database, including 114,578 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V101I) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.37 ( 10673 hom., cov: 31)

Exomes 𝑓: 0.37 ( 103905 hom. )

Consequence

FPR1
NM_002029.4 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.283

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=7.5453434E-5).

BP6

Variant 19-51746694-C-G is Benign according to our data. Variant chr19-51746694-C-G is described in ClinVar as [Benign]. Clinvar id is 402878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FPR1	NM_002029.4 linkuse as main transcript	c.301G>C	p.Val101Leu	missense_variant	2/2	ENST00000304748.5
FPR1	NM_001193306.2 linkuse as main transcript	c.301G>C	p.Val101Leu	missense_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
FPR1	ENST00000304748.5 linkuse as main transcript	c.301G>C	p.Val101Leu	missense_variant	2/2	1	NM_002029.4	P1
FPR1	ENST00000594900.2 linkuse as main transcript	c.301G>C	p.Val101Leu	missense_variant	3/3	4		P1
FPR1	ENST00000595042.5 linkuse as main transcript	c.301G>C	p.Val101Leu	missense_variant	3/3	2		P1
FPR1	ENST00000600815.2 linkuse as main transcript	c.301G>C	p.Val101Leu	missense_variant	2/2	3		P1

Frequencies

GnomAD3 genomes

AF:

0.370

AC:

56191

AN:

151790

Hom.:

10667

Cov.:

show subpopulations

Gnomad AFR

AF:

0.319

Gnomad AMI

AF:

0.176

Gnomad AMR

AF:

0.487

Gnomad ASJ

AF:

0.277

Gnomad EAS

AF:

0.483

Gnomad SAS

AF:

0.354

Gnomad FIN

AF:

0.441

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.365

Gnomad OTH

AF:

0.366

GnomAD3 exomes

AF:

0.401

AC:

100695

AN:

251342

Hom.:

21697

AF XY:

0.390

AC XY:

52939

AN XY:

135840

show subpopulations

Gnomad AFR exome

AF:

0.317

Gnomad AMR exome

AF:

0.607

Gnomad ASJ exome

AF:

0.271

Gnomad EAS exome

AF:

0.476

Gnomad SAS exome

AF:

0.347

Gnomad FIN exome

AF:

0.436

Gnomad NFE exome

AF:

0.358

Gnomad OTH exome

AF:

0.383

GnomAD4 exome

AF:

0.372

AC:

544174

AN:

1461820

Hom.:

103905

Cov.:

AF XY:

0.370

AC XY:

269277

AN XY:

727210

show subpopulations

Gnomad4 AFR exome

AF:

0.311

Gnomad4 AMR exome

AF:

0.593

Gnomad4 ASJ exome

AF:

0.272

Gnomad4 EAS exome

AF:

0.486

Gnomad4 SAS exome

AF:

0.352

Gnomad4 FIN exome

AF:

0.438

Gnomad4 NFE exome

AF:

0.363

Gnomad4 OTH exome

AF:

0.368

GnomAD4 genome

AF:

0.370

AC:

56221

AN:

151908

Hom.:

10673

Cov.:

AF XY:

0.375

AC XY:

27859

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.319

Gnomad4 AMR

AF:

0.487

Gnomad4 ASJ

AF:

0.277

Gnomad4 EAS

AF:

0.482

Gnomad4 SAS

AF:

0.353

Gnomad4 FIN

AF:

0.441

Gnomad4 NFE

AF:

0.365

Gnomad4 OTH

AF:

0.363

Alfa

AF:

0.312

Hom.:

2306

Bravo

AF:

0.375

TwinsUK

AF:

0.365

AC:

1354

ALSPAC

AF:

0.362

AC:

1394

ESP6500AA

AF:

0.315

AC:

1389

ESP6500EA

AF:

0.358

AC:

3075

ExAC

AF:

0.389

AC:

47241

EpiCase

AF:

0.350

EpiControl

AF:

0.347

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

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	-	- -

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: MAF -

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

0.33

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.72

CADD

Benign

0.20

DANN

Benign

0.35

DEOGEN2

Benign

0.049

T;T;.

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.029

LIST_S2

Benign

0.064

.;T;T

MetaRNN

Benign

0.000075

T;T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

0.96

L;L;.

MutationTaster

Benign

1.0

PrimateAI

Benign

0.41

PROVEAN

Benign

-1.0

.;N;.

REVEL

Benign

0.052

Sift

Benign

0.24

.;T;.

Sift4G

Benign

0.65

T;T;.

Polyphen

0.0010

B;B;.

Vest4

0.019

MPC

0.30

ClinPred

0.0047

GERP RS

-2.0

Varity_R

0.084

gMVP

0.33

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