rs61736491

chr19-51746818-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Moderate BP6_Moderate BP7 BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.427

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]

ACMG classification

Verdict is Benign. Variant got -13 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_single_submitter, 1 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	UniProt
FPR1	NM_002029.4	c.177C>T	p.Val59=	synonymous_variant	2/2	ENST00000304748.5
FPR1	NM_001193306.2	c.177C>T	p.Val59=	synonymous_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FPR1	ENST00000304748.5	c.177C>T	p.Val59=	synonymous_variant	2/2	1	NM_002029.4	P1
FPR1	ENST00000594900.2	c.177C>T	p.Val59=	synonymous_variant	3/3	4		P1
FPR1	ENST00000595042.5	c.177C>T	p.Val59=	synonymous_variant	3/3	2		P1
FPR1	ENST00000600815.2	c.177C>T	p.Val59=	synonymous_variant	2/2	3		P1

Frequencies

GnomAD3 genomes AF: 0.0180 AC: 2732 AN: 152132 Hom.: 67 Cov.: 31

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.: 31 AF XY: 0.00633 AC XY: 860 AN XY: 135914

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.: 86 Cov.: 76 AF XY: 0.00527 AC XY: 3836 AN XY: 727244

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.: 67 Cov.: 31 AF XY: 0.0174 AC XY: 1298 AN XY: 74442

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.: 20

Bravo AF: 0.0200

Asia WGS AF: 0.00346 AC: 13 AN: 3478

EpiCase AF: 0.00573

EpiControl AF: 0.00528

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Gingival disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 31, 2024

- -

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

Other links and lift over

dbSNP: rs61736491; hg19: chr19-52250071;