19-51745746-G-A

Variant names:

• chr19-51745746-G-A
• rs867229
• NM_001193306.2:c.*196C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001193306.2(FPR1):​c.*196C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 532,714 control chromosomes in the GnomAD database, including 10,452 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.22 (5184 hom., cov: 31)
  • Exomes 𝑓: 0.14 (5268 hom.)
• Consequence: FPR1 NM_001193306.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646
• Publications: 4 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001193306.2. 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_001193306.2		c.*196C>T		3_prime_UTR	Exon 3 of 3	NP_001180235.1
	FPR1	NM_002029.4	MANE Select	c.*196C>T		downstream_gene	N/A	NP_002020.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FPR1	ENST00000595042.5	TSL:2	c.*196C>T		3_prime_UTR	Exon 3 of 3	ENSP00000471493.1
	FPR1	ENST00000304748.5	TSL:1 MANE Select	c.*196C>T		downstream_gene	N/A	ENSP00000302707.3
	FPR1	ENST00000594900.2	TSL:4	c.*196C>T		downstream_gene	N/A	ENSP00000470750.2

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32664 AN: 151460 Hom.: 5152 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.112

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.204

GnomAD4 exome AF: 0.141 AC: 53803 AN: 381152 Hom.: 5268 Cov.: 4 AF XY: 0.139 AC XY: 27532 AN XY: 198742

African (AFR) AF: 0.444 AC: 5132 AN: 11554

American (AMR) AF: 0.141 AC: 2092 AN: 14840

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 1831 AN: 11980

East Asian (EAS) AF: 0.349 AC: 9298 AN: 26650

South Asian (SAS) AF: 0.125 AC: 4335 AN: 34698

European-Finnish (FIN) AF: 0.147 AC: 3583 AN: 24354

Middle Eastern (MID) AF: 0.107 AC: 179 AN: 1678

European-Non Finnish (NFE) AF: 0.103 AC: 23947 AN: 233152

Other (OTH) AF: 0.153 AC: 3406 AN: 22246

GnomAD4 genome AF: 0.216 AC: 32752 AN: 151562 Hom.: 5184 Cov.: 31 AF XY: 0.216 AC XY: 16007 AN XY: 73990

African (AFR) AF: 0.447 AC: 18482 AN: 41306

American (AMR) AF: 0.151 AC: 2294 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 552 AN: 3470

East Asian (EAS) AF: 0.322 AC: 1657 AN: 5140

South Asian (SAS) AF: 0.143 AC: 684 AN: 4796

European-Finnish (FIN) AF: 0.158 AC: 1636 AN: 10366

Middle Eastern (MID) AF: 0.115 AC: 33 AN: 288

European-Non Finnish (NFE) AF: 0.102 AC: 6903 AN: 67942

Other (OTH) AF: 0.210 AC: 441 AN: 2102

Alfa AF: 0.136 Hom.: 873

Bravo AF: 0.226

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.66
PhyloP100		0.65
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: rs867229; hg19: chr19-52248999;