19-51746223-G-T

Position:

• chr19-51746223-G-T

Variant summary

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

The NM_002029.4(FPR1):​c.772C>A​(p.Gln258Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FPR1 NM_002029.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.07

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 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FPR1	NM_002029.4	c.772C>A	p.Gln258Lys	missense_variant	2/2	ENST00000304748.5
FPR1	NM_001193306.2	c.772C>A	p.Gln258Lys	missense_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FPR1	ENST00000304748.5	c.772C>A	p.Gln258Lys	missense_variant	2/2	1	NM_002029.4	P1
FPR1	ENST00000594900.2	c.772C>A	p.Gln258Lys	missense_variant	3/3	4		P1
FPR1	ENST00000595042.5	c.772C>A	p.Gln258Lys	missense_variant	3/3	2		P1
FPR1	ENST00000600815.2	c.772C>A	p.Gln258Lys	missense_variant	2/2	3		P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 72

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.88
BayesDel_addAF	Benign	-0.048	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	23
DANN	Benign	0.97
DEOGEN2	Benign	0.15	T;T
Eigen	Uncertain	0.42
Eigen_PC	Uncertain	0.23
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Benign	0.76	.;T
M_CAP	Benign	0.013	T
MetaRNN	Uncertain	0.60	D;D
MetaSVM	Benign	-0.40	T
MutationAssessor	Pathogenic	3.3	M;M
MutationTaster	Benign	0.99	D
PrimateAI	Benign	0.40	T
PROVEAN	Benign	-2.0	.;N
REVEL	Benign	0.27
Sift	Benign	0.039	.;D
Sift4G	Uncertain	0.046	D;D
Polyphen		0.83	P;P
Vest4		0.30
MutPred		0.78		Gain of ubiquitination at Q258 (P = 0.0267);Gain of ubiquitination at Q258 (P = 0.0267);
MVP		0.83
MPC		0.77
ClinPred		0.97	D
GERP RS		3.5
Varity_R		0.69
gMVP		0.30

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: rs193920896; hg19: chr19-52249476;