rs5030878

chr19-51746963-A-Cchr19-51746963-A-Gchr19-51746963-A-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002029.4(FPR1):c.32T>G(p.Ile11Ser) 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. 14/22 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. I11T) has been classified as Benign.

• Frequency: Genomes: not found (cov: 29)
• Consequence: FPR1 NM_002029.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.027597994).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FPR1	NM_002029.4	c.32T>G	p.Ile11Ser	missense_variant	2/2	ENST00000304748.5
FPR1	NM_001193306.2	c.32T>G	p.Ile11Ser	missense_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FPR1	ENST00000304748.5	c.32T>G	p.Ile11Ser	missense_variant	2/2	1	NM_002029.4	P1
FPR1	ENST00000594900.2	c.32T>G	p.Ile11Ser	missense_variant	3/3	4		P1
FPR1	ENST00000595042.5	c.32T>G	p.Ile11Ser	missense_variant	3/3	2		P1
FPR1	ENST00000600815.2	c.32T>G	p.Ile11Ser	missense_variant	2/2	3		P1

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Cov.: 51

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.65
Cadd	Benign	0.052
Dann	Benign	0.65
DEOGEN2	Benign	0.050	T;T;.;.
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.014	N
M_CAP	Benign	0.0046	T
MetaRNN	Benign	0.028	T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.34	N;N;.;.
MutationTaster	Benign	1.0	N
PrimateAI	Benign	0.24	T
Sift4G	Benign	0.89	T;T;.;.
Polyphen		0.0010	B;B;.;.
Vest4		0.14
MutPred		0.36		Gain of disorder (P = 0.0052);Gain of disorder (P = 0.0052);Gain of disorder (P = 0.0052);Gain of disorder (P = 0.0052);
MVP		0.099
MPC		0.44
ClinPred		0.073	T
GERP RS		-6.9
Varity_R		0.045
gMVP		0.20

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.25		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.25		Position offset: -1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5030878; hg19: chr19-52250216;