19-51746507-C-A

Position:

• chr19-51746507-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_002029.4(FPR1):​c.488G>T​(p.Arg163Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R163H) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FPR1 NM_002029.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.92

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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.25849715).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FPR1	NM_002029.4	c.488G>T	p.Arg163Leu	missense_variant	2/2	ENST00000304748.5
FPR1	NM_001193306.2	c.488G>T	p.Arg163Leu	missense_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FPR1	ENST00000304748.5	c.488G>T	p.Arg163Leu	missense_variant	2/2	1	NM_002029.4	P1
FPR1	ENST00000594900.2	c.488G>T	p.Arg163Leu	missense_variant	3/3	4		P1
FPR1	ENST00000595042.5	c.488G>T	p.Arg163Leu	missense_variant	3/3	2		P1
FPR1	ENST00000600815.2	c.488G>T	p.Arg163Leu	missense_variant	2/2	3		P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 76

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.59
BayesDel_addAF	Benign	-0.063	T
BayesDel_noAF	Benign	-0.33
CADD	Benign	5.9
DANN	Uncertain	0.98
DEOGEN2	Benign	0.038	T;T;.
Eigen	Benign	-0.78
Eigen_PC	Benign	-0.81
FATHMM_MKL	Benign	0.086	N
LIST_S2	Benign	0.56	.;T;T
M_CAP	Benign	0.020	T
MetaRNN	Benign	0.26	T;T;T
MetaSVM	Benign	-0.91	T
MutationAssessor	Benign	0.53	N;N;.
MutationTaster	Benign	0.97	N
PrimateAI	Benign	0.26	T
PROVEAN	Benign	1.1	.;N;.
REVEL	Benign	0.17
Sift	Benign	0.057	.;T;.
Sift4G	Benign	0.17	T;T;.
Polyphen		0.010	B;B;.
Vest4		0.28
MutPred		0.66		Gain of glycosylation at T166 (P = 0.0555);Gain of glycosylation at T166 (P = 0.0555);Gain of glycosylation at T166 (P = 0.0555);
MVP		0.76
MPC		0.38
ClinPred		0.25	T
GERP RS		2.6
Varity_R		0.076
gMVP		0.58

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: rs111768566; hg19: chr19-52249760;