rs5030879

Positions:

• chr19-51746647-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BA1

The NM_002029.4(FPR1):​c.348C>T​(p.Ile116=) 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.08

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 -15 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_single_submitter, 1 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	UniProt
FPR1	NM_002029.4	c.348C>T	p.Ile116=	synonymous_variant	2/2	ENST00000304748.5
FPR1	NM_001193306.2	c.348C>T	p.Ile116=	synonymous_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FPR1	ENST00000304748.5	c.348C>T	p.Ile116=	synonymous_variant	2/2	1	NM_002029.4	P1
FPR1	ENST00000594900.2	c.348C>T	p.Ile116=	synonymous_variant	3/3	4		P1
FPR1	ENST00000595042.5	c.348C>T	p.Ile116=	synonymous_variant	3/3	2		P1
FPR1	ENST00000600815.2	c.348C>T	p.Ile116=	synonymous_variant	2/2	3		P1

Frequencies

GnomAD3 genomes AF: 0.0896 AC: 13620 AN: 152010 Hom.: 1925 Cov.: 32

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

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.: 76 AF XY: 0.0124 AC XY: 9018 AN XY: 727246

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.: 32 AF XY: 0.0868 AC XY: 6458 AN XY: 74380

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: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	-0.56
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

Other links and lift over

dbSNP: rs5030879; hg19: chr19-52249900; COSMIC: COSV59051850; COSMIC: COSV59051850;