dbSNP rs28930680: FPR1:p.Phe102Phe (chr19-51746689-A-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_002029.4(FPR1):c.306T>C(p.Phe102Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0389 in 1,614,162 control chromosomes in the GnomAD database, including 1,600 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.030 ( 109 hom., cov: 32)

Exomes 𝑓: 0.040 ( 1491 hom. )

Consequence

FPR1
NM_002029.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0970

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 19-51746689-A-G is Benign according to our data. Variant chr19-51746689-A-G is described in ClinVar as [Benign]. Clinvar id is 456365.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.097 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FPR1	NM_002029.4 link	c.306T>C	p.Phe102Phe	synonymous_variant	Exon 2 of 2	ENST00000304748.5	NP_002020.1	P21462
FPR1	NM_001193306.2 link	c.306T>C	p.Phe102Phe	synonymous_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.306T>C	p.Phe102Phe	synonymous_variant	Exon 2 of 2	1	NM_002029.4	ENSP00000302707.3	P21462
FPR1	ENST00000594900.2 link	c.306T>C	p.Phe102Phe	synonymous_variant	Exon 3 of 3	4		ENSP00000470750.2	P21462M0QZT0
FPR1	ENST00000595042.5 link	c.306T>C	p.Phe102Phe	synonymous_variant	Exon 3 of 3	2		ENSP00000471493.1	P21462
FPR1	ENST00000600815.2 link	c.306T>C	p.Phe102Phe	synonymous_variant	Exon 2 of 2	3		ENSP00000472936.2	P21462M0R315

Frequencies

GnomAD3 genomes

AF:

0.0301

AC:

4578

AN:

152160

Hom.:

105

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00693

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0293

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.0143

Gnomad SAS

AF:

0.0690

Gnomad FIN

AF:

0.0217

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0394

Gnomad OTH

AF:

0.0368

GnomAD3 exomes

AF:

0.0421

AC:

10589

AN:

251370

Hom.:

331

AF XY:

0.0459

AC XY:

6239

AN XY:

135854

show subpopulations

Gnomad AFR exome

AF:

0.00597

Gnomad AMR exome

AF:

0.0252

Gnomad ASJ exome

AF:

0.120

Gnomad EAS exome

AF:

0.0151

Gnomad SAS exome

AF:

0.0803

Gnomad FIN exome

AF:

0.0231

Gnomad NFE exome

AF:

0.0425

Gnomad OTH exome

AF:

0.0567

GnomAD4 exome

AF:

0.0398

AC:

58246

AN:

1461884

Hom.:

1491

Cov.:

AF XY:

0.0415

AC XY:

30178

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.00514

Gnomad4 AMR exome

AF:

0.0264

Gnomad4 ASJ exome

AF:

0.120

Gnomad4 EAS exome

AF:

0.0109

Gnomad4 SAS exome

AF:

0.0809

Gnomad4 FIN exome

AF:

0.0227

Gnomad4 NFE exome

AF:

0.0376

Gnomad4 OTH exome

AF:

0.0452

GnomAD4 genome

AF:

0.0301

AC:

4591

AN:

152278

Hom.:

109

Cov.:

AF XY:

0.0299

AC XY:

2224

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00691

Gnomad4 AMR

AF:

0.0292

Gnomad4 ASJ

AF:

0.119

Gnomad4 EAS

AF:

0.0145

Gnomad4 SAS

AF:

0.0690

Gnomad4 FIN

AF:

0.0217

Gnomad4 NFE

AF:

0.0394

Gnomad4 OTH

AF:

0.0440

Alfa

AF:

0.0400

Hom.:

Bravo

AF:

0.0291

Asia WGS

AF:

0.0680

AC:

235

AN:

3478

EpiCase

AF:

0.0444

EpiControl

AF:

0.0506

ClinVar

Significance: Benign

Submissions summary: Benign:2

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

- -

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

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.20

DANN

Benign

0.32

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