Variant chr19-51746818-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_002029.4(FPR1):c.177C>T(p.Val59=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00676 in 1,614,136 control chromosomes in the GnomAD database, including 153 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 67 hom., cov: 31)

Exomes 𝑓: 0.0056 ( 86 hom. )

Consequence

FPR1
NM_002029.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.427

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 19-51746818-G-A is Benign according to our data. Variant chr19-51746818-G-A is described in ClinVar as [Benign]. Clinvar id is 456363.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.427 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0518 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.177C>T	p.Val59=	synonymous_variant	2/2	ENST00000304748.5	NP_002020.1
FPR1	NM_001193306.2 linkuse as main transcript	c.177C>T	p.Val59=	synonymous_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.177C>T	p.Val59=	synonymous_variant	2/2	1	NM_002029.4	ENSP00000302707	P1
FPR1	ENST00000594900.2 linkuse as main transcript	c.177C>T	p.Val59=	synonymous_variant	3/3	4		ENSP00000470750	P1
FPR1	ENST00000595042.5 linkuse as main transcript	c.177C>T	p.Val59=	synonymous_variant	3/3	2		ENSP00000471493	P1
FPR1	ENST00000600815.2 linkuse as main transcript	c.177C>T	p.Val59=	synonymous_variant	2/2	3		ENSP00000472936	P1

Frequencies

GnomAD3 genomes

AF:

0.0180

AC:

2732

AN:

152132

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0510

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0107

Gnomad ASJ

AF:

0.0115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000829

Gnomad FIN

AF:

0.00170

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00522

Gnomad OTH

AF:

0.0158

GnomAD3 exomes

AF:

0.00741

AC:

1863

AN:

251478

Hom.:

AF XY:

0.00633

AC XY:

860

AN XY:

135914

show subpopulations

Gnomad AFR exome

AF:

0.0523

Gnomad AMR exome

AF:

0.00627

Gnomad ASJ exome

AF:

0.00943

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000915

Gnomad FIN exome

AF:

0.00176

Gnomad NFE exome

AF:

0.00516

Gnomad OTH exome

AF:

0.00766

GnomAD4 exome

AF:

0.00559

AC:

8172

AN:

1461884

Hom.:

Cov.:

AF XY:

0.00527

AC XY:

3836

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.0539

Gnomad4 AMR exome

AF:

0.00622

Gnomad4 ASJ exome

AF:

0.00872

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00102

Gnomad4 FIN exome

AF:

0.00170

Gnomad4 NFE exome

AF:

0.00467

Gnomad4 OTH exome

AF:

0.00755

GnomAD4 genome

AF:

0.0180

AC:

2737

AN:

152252

Hom.:

Cov.:

AF XY:

0.0174

AC XY:

1298

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.0510

Gnomad4 AMR

AF:

0.0107

Gnomad4 ASJ

AF:

0.0115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000829

Gnomad4 FIN

AF:

0.00170

Gnomad4 NFE

AF:

0.00522

Gnomad4 OTH

AF:

0.0157

Alfa

AF:

0.0128

Hom.:

Bravo

AF:

0.0200

Asia WGS

AF:

0.00346

AC:

AN:

3478

EpiCase

AF:

0.00573

EpiControl

AF:

0.00528

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Gingival disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

1.4

DANN

Benign

0.71

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