Variant 19-51746419-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_002029.4(FPR1):c.576T>C(p.Asn192=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 1,613,884 control chromosomes in the GnomAD database, including 14,053 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 1184 hom., cov: 31)

Exomes 𝑓: 0.13 ( 12869 hom. )

Consequence

FPR1
NM_002029.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1O:1

Conservation

PhyloP100: 0.296

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 -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 19-51746419-A-G is Benign according to our data. Variant chr19-51746419-A-G is described in ClinVar as [Benign]. Clinvar id is 1168164.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.296 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 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.576T>C	p.Asn192=	synonymous_variant	2/2	ENST00000304748.5
FPR1	NM_001193306.2 linkuse as main transcript	c.576T>C	p.Asn192=	synonymous_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
FPR1	ENST00000304748.5 linkuse as main transcript	c.576T>C	p.Asn192=	synonymous_variant	2/2	1	NM_002029.4	P1
FPR1	ENST00000594900.2 linkuse as main transcript	c.576T>C	p.Asn192=	synonymous_variant	3/3	4		P1
FPR1	ENST00000595042.5 linkuse as main transcript	c.576T>C	p.Asn192=	synonymous_variant	3/3	2		P1
FPR1	ENST00000600815.2 linkuse as main transcript	c.576T>C	p.Asn192=	synonymous_variant	2/2	3		P1

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18361

AN:

151898

Hom.:

1184

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0882

Gnomad AMI

AF:

0.195

Gnomad AMR

AF:

0.0989

Gnomad ASJ

AF:

0.120

Gnomad EAS

AF:

0.199

Gnomad SAS

AF:

0.176

Gnomad FIN

AF:

0.172

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.127

Gnomad OTH

AF:

0.122

GnomAD3 exomes

AF:

0.132

AC:

33056

AN:

251308

Hom.:

2449

AF XY:

0.135

AC XY:

18341

AN XY:

135826

show subpopulations

Gnomad AFR exome

AF:

0.0839

Gnomad AMR exome

AF:

0.0840

Gnomad ASJ exome

AF:

0.118

Gnomad EAS exome

AF:

0.196

Gnomad SAS exome

AF:

0.180

Gnomad FIN exome

AF:

0.158

Gnomad NFE exome

AF:

0.126

Gnomad OTH exome

AF:

0.123

GnomAD4 exome

AF:

0.129

AC:

189146

AN:

1461868

Hom.:

12869

Cov.:

AF XY:

0.131

AC XY:

94974

AN XY:

727236

show subpopulations

Gnomad4 AFR exome

AF:

0.0840

Gnomad4 AMR exome

AF:

0.0865

Gnomad4 ASJ exome

AF:

0.119

Gnomad4 EAS exome

AF:

0.161

Gnomad4 SAS exome

AF:

0.179

Gnomad4 FIN exome

AF:

0.165

Gnomad4 NFE exome

AF:

0.126

Gnomad4 OTH exome

AF:

0.132

GnomAD4 genome

AF:

0.121

AC:

18366

AN:

152016

Hom.:

1184

Cov.:

AF XY:

0.125

AC XY:

9271

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.0882

Gnomad4 AMR

AF:

0.0989

Gnomad4 ASJ

AF:

0.120

Gnomad4 EAS

AF:

0.198

Gnomad4 SAS

AF:

0.177

Gnomad4 FIN

AF:

0.172

Gnomad4 NFE

AF:

0.127

Gnomad4 OTH

AF:

0.123

Alfa

AF:

0.00761

Hom.:

25591

EpiCase

AF:

0.123

EpiControl

AF:

0.123

ClinVar

Significance: Benign

Submissions summary: Benign:1Other:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Gingival disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 31, 2024

- -

not provided

Other: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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.87

DANN

Benign

0.41

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