rs2070746

Variant names:

• chr19-51746449-G-T
• rs2070746
• NM_002029.4:c.546C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-51746449-G-T
• chr19-51746449-G-A
• chr19-51746449-G-C

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.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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3 O:1
• Conservation: PhyloP100: -0.164
• Publications: 27 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=-0.68).
• 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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FPR1	NM_002029.4	MANE Select	c.546C>A	p.Pro182Pro	synonymous	Exon 2 of 2	NP_002020.1	P21462
	FPR1	NM_001193306.2		c.546C>A	p.Pro182Pro	synonymous	Exon 3 of 3	NP_001180235.1	P21462

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FPR1	ENST00000304748.5	TSL:1 MANE Select	c.546C>A	p.Pro182Pro	synonymous	Exon 2 of 2	ENSP00000302707.3	P21462
	FPR1	ENST00000594900.2	TSL:4	c.546C>A	p.Pro182Pro	synonymous	Exon 3 of 3	ENSP00000470750.2	P21462
	FPR1	ENST00000595042.5	TSL:2	c.546C>A	p.Pro182Pro	synonymous	Exon 3 of 3	ENSP00000471493.1	P21462

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46757 AN: 151862 Hom.: 7306 Cov.: 31

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

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.: 76 AF XY: 0.299 AC XY: 217178 AN XY: 727236

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

GnomAD4 genome AF: 0.308 AC: 46797 AN: 151980 Hom.: 7316 Cov.: 31 AF XY: 0.309 AC XY: 22928 AN XY: 74284

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: 86 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19279 AN: 67974

Other (OTH) AF: 0.287 AC: 606 AN: 2114

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

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	1	Gingival disorder (1)
-	-	1	not provided (2)
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		-0.16
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: rs2070746; hg19: chr19-52249702; COSMIC: COSV59054342; COSMIC: COSV59054342;