19-51746419-A-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_002029.4(FPR1):c.576T>C(p.Asn192Asn) 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, multiple submitters, no conflicts B:2O:1

Conservation

PhyloP100: 0.296

Publications

52 publications found

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 Gene-Disease associations (from GenCC):

susceptibility to localized juvenile periodontitis
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Tourette syndrome
Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

FPR1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 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_multiple_submitters_no_conflicts, 2 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 rank	MANE	Protein	UniProt
FPR1	NM_002029.4 link	c.576T>C	p.Asn192Asn	synonymous_variant	Exon 2 of 2	ENST00000304748.5	NP_002020.1	P21462
FPR1	NM_001193306.2 link	c.576T>C	p.Asn192Asn	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.576T>C	p.Asn192Asn	synonymous_variant	Exon 2 of 2	1	NM_002029.4	ENSP00000302707.3	P21462
FPR1	ENST00000594900.2 link	c.576T>C	p.Asn192Asn	synonymous_variant	Exon 3 of 3	4		ENSP00000470750.2	P21462M0QZT0
FPR1	ENST00000595042.5 link	c.576T>C	p.Asn192Asn	synonymous_variant	Exon 3 of 3	2		ENSP00000471493.1	P21462
FPR1	ENST00000600815.2 link	c.576T>C	p.Asn192Asn	synonymous_variant	Exon 2 of 2	3		ENSP00000472936.2	P21462M0R315

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

GnomAD2 exomes

AF:

0.132

AC:

33056

AN:

251308

AF XY:

0.135

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 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

African (AFR)

AF:

0.0840

AC:

2812

AN:

33480

American (AMR)

AF:

0.0865

AC:

3867

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.119

AC:

3121

AN:

26136

East Asian (EAS)

AF:

0.161

AC:

6384

AN:

39700

South Asian (SAS)

AF:

0.179

AC:

15403

AN:

86258

European-Finnish (FIN)

AF:

0.165

AC:

8810

AN:

53416

Middle Eastern (MID)

AF:

0.0862

AC:

497

AN:

5766

European-Non Finnish (NFE)

AF:

0.126

AC:

140267

AN:

1111992

Other (OTH)

AF:

0.132

AC:

7985

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

10992

21984

32977

43969

54961

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.121

AC:

18366

AN:

152016

Hom.:

1184

Cov.:

AF XY:

0.125

AC XY:

9271

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.0882

AC:

3655

AN:

41458

American (AMR)

AF:

0.0989

AC:

1512

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.120

AC:

414

AN:

3464

East Asian (EAS)

AF:

0.198

AC:

1018

AN:

5140

South Asian (SAS)

AF:

0.177

AC:

851

AN:

4816

European-Finnish (FIN)

AF:

0.172

AC:

1820

AN:

10572

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.127

AC:

8616

AN:

67956

Other (OTH)

AF:

0.123

AC:

261

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

825

1650

2475

3300

4125

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00485

Hom.:

41618

EpiCase

AF:

0.123

EpiControl

AF:

0.123

ClinVar

Significance: Benign

Submissions summary: Benign:2Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1Other:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

GenomeConnect, ClinGen

Significance:not provided

Review Status:no classification provided

Collection Method:phenotyping only

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. -

Gingival disorder

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.87

(source)

DANN

Benign

0.41

PhyloP100

0.30

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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19-51746419-A-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over