rs867229

Positions:

• chr19-51745746-G-A
• chr19-51745746-G-T

Variant summary

Our verdict is Benign. Variant got -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

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FPR1	NM_001193306.2	c.*196C>T		3_prime_UTR_variant	3/3
FPR1	NM_002029.4			downstream_gene_variant		ENST00000304748.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FPR1	ENST00000595042.5	c.*196C>T		3_prime_UTR_variant	3/3	2		P1
FPR1	ENST00000304748.5			downstream_gene_variant		1	NM_002029.4	P1
FPR1	ENST00000594900.2			downstream_gene_variant		4		P1
FPR1	ENST00000600815.2			downstream_gene_variant		3		P1

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

Gnomad4 AFR exome AF: 0.444

Gnomad4 AMR exome AF: 0.141

Gnomad4 ASJ exome AF: 0.153

Gnomad4 EAS exome AF: 0.349

Gnomad4 SAS exome AF: 0.125

Gnomad4 FIN exome AF: 0.147

Gnomad4 NFE exome AF: 0.103

Gnomad4 OTH exome AF: 0.153

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

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.210

Alfa AF: 0.108 Hom.: 368

Bravo AF: 0.226

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.66

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: rs867229; hg19: chr19-52248999;