19-51746647-G-A

Variant names:

• chr19-51746647-G-A
• rs5030879
• NM_002029.4:c.348C>T

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.08
• Publications: 14 publications found

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)

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002029.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FPR1	NM_002029.4	MANE Select	c.348C>T	p.Ile116Ile	synonymous	Exon 2 of 2	NP_002020.1
	FPR1	NM_001193306.2		c.348C>T	p.Ile116Ile	synonymous	Exon 3 of 3	NP_001180235.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FPR1	ENST00000304748.5	TSL:1 MANE Select	c.348C>T	p.Ile116Ile	synonymous	Exon 2 of 2	ENSP00000302707.3
	FPR1	ENST00000594900.2	TSL:4	c.348C>T	p.Ile116Ile	synonymous	Exon 3 of 3	ENSP00000470750.2
	FPR1	ENST00000595042.5	TSL:2	c.348C>T	p.Ile116Ile	synonymous	Exon 3 of 3	ENSP00000471493.1

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

GnomAD2 exomes AF: 0.0285 AC: 7157 AN: 251290 AF XY: 0.0228

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 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

African (AFR) AF: 0.315 AC: 10554 AN: 33480

American (AMR) AF: 0.0212 AC: 950 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.0113 AC: 296 AN: 26136

East Asian (EAS) AF: 0.000605 AC: 24 AN: 39700

South Asian (SAS) AF: 0.0191 AC: 1651 AN: 86258

European-Finnish (FIN) AF: 0.000431 AC: 23 AN: 53420

Middle Eastern (MID) AF: 0.0414 AC: 239 AN: 5768

European-Non Finnish (NFE) AF: 0.00367 AC: 4085 AN: 1112008

Other (OTH) AF: 0.0255 AC: 1538 AN: 60396

GnomAD4 genome AF: 0.0898 AC: 13661 AN: 152128 Hom.: 1929 Cov.: 32 AF XY: 0.0868 AC XY: 6458 AN XY: 74380

African (AFR) AF: 0.301 AC: 12482 AN: 41424

American (AMR) AF: 0.0367 AC: 562 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00979 AC: 34 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5178

South Asian (SAS) AF: 0.0141 AC: 68 AN: 4816

European-Finnish (FIN) AF: 0.000283 AC: 3 AN: 10610

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00478 AC: 325 AN: 68020

Other (OTH) AF: 0.0784 AC: 165 AN: 2104

Alfa AF: 0.0747 Hom.: 1353

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

Submissions by phenotype

Gingival disorder Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

not provided Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	0.41
DANN	Benign	0.77
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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