Variant rs5030879 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_002029.4(FPR1):c.348C>T(p.Ile116Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0205 in 1,614,018 control chromosomes in the GnomAD database, including 3,791 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.090 ( 1929 hom., cov: 32)

Exomes 𝑓: 0.013 ( 1862 hom. )

Consequence

FPR1
NM_002029.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.08

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=-0.56).

BP6

Variant 19-51746647-G-A is Benign according to our data. Variant chr19-51746647-G-A is described in ClinVar as [Benign]. Clinvar id is 456366.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.08 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 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.348C>T	p.Ile116Ile	synonymous_variant	2/2	ENST00000304748.5	NP_002020.1	P21462
FPR1	NM_001193306.2 linkuse as main transcript	c.348C>T	p.Ile116Ile	synonymous_variant	3/3		NP_001180235.1	P21462

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
FPR1	ENST00000304748.5 linkuse as main transcript	c.348C>T	p.Ile116Ile	synonymous_variant	2/2	1	NM_002029.4	ENSP00000302707.3	P21462
FPR1	ENST00000594900.2 linkuse as main transcript	c.348C>T	p.Ile116Ile	synonymous_variant	3/3	4		ENSP00000470750.2	P21462M0QZT0
FPR1	ENST00000595042.5 linkuse as main transcript	c.348C>T	p.Ile116Ile	synonymous_variant	3/3	2		ENSP00000471493.1	P21462
FPR1	ENST00000600815.2 linkuse as main transcript	c.348C>T	p.Ile116Ile	synonymous_variant	2/2	3		ENSP00000472936.2	P21462M0R315

Frequencies

GnomAD3 genomes

AF:

0.0896

AC:

13620

AN:

152010

Hom.:

1925

Cov.:

show subpopulations

Gnomad AFR

AF:

0.301

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0369

Gnomad ASJ

AF:

0.00979

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.0143

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.00478

Gnomad OTH

AF:

0.0759

GnomAD3 exomes

AF:

0.0285

AC:

7157

AN:

251290

Hom.:

806

AF XY:

0.0228

AC XY:

3090

AN XY:

135816

show subpopulations

Gnomad AFR exome

AF:

0.310

Gnomad AMR exome

AF:

0.0191

Gnomad ASJ exome

AF:

0.0112

Gnomad EAS exome

AF:

0.000924

Gnomad SAS exome

AF:

0.0187

Gnomad FIN exome

AF:

0.000231

Gnomad NFE exome

AF:

0.00539

Gnomad OTH exome

AF:

0.0220

GnomAD4 exome

AF:

0.0132

AC:

19360

AN:

1461890

Hom.:

1862

Cov.:

AF XY:

0.0124

AC XY:

9018

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.315

Gnomad4 AMR exome

AF:

0.0212

Gnomad4 ASJ exome

AF:

0.0113

Gnomad4 EAS exome

AF:

0.000605

Gnomad4 SAS exome

AF:

0.0191

Gnomad4 FIN exome

AF:

0.000431

Gnomad4 NFE exome

AF:

0.00367

Gnomad4 OTH exome

AF:

0.0255

GnomAD4 genome

AF:

0.0898

AC:

13661

AN:

152128

Hom.:

1929

Cov.:

AF XY:

0.0868

AC XY:

6458

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.301

Gnomad4 AMR

AF:

0.0367

Gnomad4 ASJ

AF:

0.00979

Gnomad4 EAS

AF:

0.00154

Gnomad4 SAS

AF:

0.0141

Gnomad4 FIN

AF:

0.000283

Gnomad4 NFE

AF:

0.00478

Gnomad4 OTH

AF:

0.0784

Alfa

AF:

0.0513

Hom.:

622

Bravo

AF:

0.102

Asia WGS

AF:

0.0490

AC:

170

AN:

3478

EpiCase

AF:

0.00780

EpiControl

AF:

0.00741

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

-0.56

CADD

Benign

0.41

DANN

Benign

0.77

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