chr19-51746449-G-T

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.546C>A(p.Pro182Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 1,613,844 control chromosomes in the GnomAD database, including 74,947 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 7316 hom., cov: 31)

Exomes 𝑓: 0.30 ( 67631 hom. )

Consequence

FPR1
NM_002029.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3O:1

Conservation

PhyloP100: -0.164

Publications

25 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=-0.68).

BP6

Variant 19-51746449-G-T is Benign according to our data. Variant chr19-51746449-G-T is described in ClinVar as Benign. ClinVar VariationId is 402877.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.164 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FPR1	NM_002029.4 link	c.546C>A	p.Pro182Pro	synonymous_variant	Exon 2 of 2	ENST00000304748.5	NP_002020.1	P21462
FPR1	NM_001193306.2 link	c.546C>A	p.Pro182Pro	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.546C>A	p.Pro182Pro	synonymous_variant	Exon 2 of 2	1	NM_002029.4	ENSP00000302707.3	P21462
FPR1	ENST00000594900.2 link	c.546C>A	p.Pro182Pro	synonymous_variant	Exon 3 of 3	4		ENSP00000470750.2	P21462M0QZT0
FPR1	ENST00000595042.5 link	c.546C>A	p.Pro182Pro	synonymous_variant	Exon 3 of 3	2		ENSP00000471493.1	P21462
FPR1	ENST00000600815.2 link	c.546C>A	p.Pro182Pro	synonymous_variant	Exon 2 of 2	3		ENSP00000472936.2	P21462M0R315

Frequencies

GnomAD3 genomes

AF:

0.308

AC:

46757

AN:

151862

Hom.:

7306

Cov.:

show subpopulations

Gnomad AFR

AF:

0.303

Gnomad AMI

AF:

0.180

Gnomad AMR

AF:

0.399

Gnomad ASJ

AF:

0.327

Gnomad EAS

AF:

0.466

Gnomad SAS

AF:

0.332

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.284

Gnomad OTH

AF:

0.283

GnomAD2 exomes

AF:

0.338

AC:

85060

AN:

251310

AF XY:

0.330

show subpopulations

Gnomad AFR exome

AF:

0.304

Gnomad AMR exome

AF:

0.505

Gnomad ASJ exome

AF:

0.341

Gnomad EAS exome

AF:

0.487

Gnomad FIN exome

AF:

0.298

Gnomad NFE exome

AF:

0.280

Gnomad OTH exome

AF:

0.301

GnomAD4 exome

AF:

0.299

AC:

437211

AN:

1461864

Hom.:

67631

Cov.:

AF XY:

0.299

AC XY:

217178

AN XY:

727236

show subpopulations

African (AFR)

AF:

0.299

AC:

10025

AN:

33480

American (AMR)

AF:

0.489

AC:

21857

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.338

AC:

8827

AN:

26136

East Asian (EAS)

AF:

0.480

AC:

19060

AN:

39700

South Asian (SAS)

AF:

0.324

AC:

27961

AN:

86258

European-Finnish (FIN)

AF:

0.291

AC:

15567

AN:

53410

Middle Eastern (MID)

AF:

0.229

AC:

1319

AN:

5768

European-Non Finnish (NFE)

AF:

0.283

AC:

314956

AN:

1111992

Other (OTH)

AF:

0.292

AC:

17639

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

19951

39902

59854

79805

99756

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10770

21540

32310

43080

53850

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.308

AC:

46797

AN:

151980

Hom.:

7316

Cov.:

AF XY:

0.309

AC XY:

22928

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.303

AC:

12556

AN:

41452

American (AMR)

AF:

0.399

AC:

6093

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.327

AC:

1132

AN:

3464

East Asian (EAS)

AF:

0.466

AC:

2391

AN:

5132

South Asian (SAS)

AF:

0.332

AC:

1594

AN:

4808

European-Finnish (FIN)

AF:

0.274

AC:

2896

AN:

10570

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.284

AC:

19279

AN:

67974

Other (OTH)

AF:

0.287

AC:

606

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1665

3330

4994

6659

8324

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

472

944

1416

1888

2360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.291

Hom.:

16569

Bravo

AF:

0.318

Asia WGS

AF:

0.393

AC:

1363

AN:

3478

EpiCase

AF:

0.270

EpiControl

AF:

0.270

ClinVar

Significance: Benign

Submissions summary: Benign:3Other: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. -

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

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

-0.68

CADD

Benign

1.8

(source)

DANN

Benign

0.56

PhyloP100

-0.16

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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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