chr19-51746963-A-T

Position:

• chr19-51746963-A-T

Variant summary

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

The ENST00000304748.5(FPR1):​c.32T>A​(p.Ile11Asn) 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. 15/21 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. I11T) has been classified as Benign.

• Frequency: Genomes: not found (cov: 29)
• Consequence: FPR1 ENST00000304748.5 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=0.031732142).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FPR1	NM_002029.4	c.32T>A	p.Ile11Asn	missense_variant	2/2	ENST00000304748.5	NP_002020.1
FPR1	NM_001193306.2	c.32T>A	p.Ile11Asn	missense_variant	3/3		NP_001180235.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FPR1	ENST00000304748.5	c.32T>A	p.Ile11Asn	missense_variant	2/2	1	NM_002029.4	ENSP00000302707	P1
FPR1	ENST00000594900.2	c.32T>A	p.Ile11Asn	missense_variant	3/3	4		ENSP00000470750	P1
FPR1	ENST00000595042.5	c.32T>A	p.Ile11Asn	missense_variant	3/3	2		ENSP00000471493	P1
FPR1	ENST00000600815.2	c.32T>A	p.Ile11Asn	missense_variant	2/2	3		ENSP00000472936	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	-0.32	T
BayesDel_noAF	Benign	-0.70
CADD	Benign	0.013
DANN	Benign	0.73
DEOGEN2	Benign	0.084	T;T;.;.
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.013	N
LIST_S2	Benign	0.36	.;T;T;T
M_CAP	Benign	0.0064	T
MetaRNN	Benign	0.032	T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	-0.34	N;N;.;.
MutationTaster	Benign	1.0	N
PrimateAI	Benign	0.25	T
PROVEAN	Benign	0.32	.;N;.;.
REVEL	Benign	0.026
Sift	Benign	0.53	.;T;.;.
Sift4G	Benign	0.63	T;T;.;.
Polyphen		0.017	B;B;.;.
Vest4		0.15
MutPred		0.33		Gain of disorder (P = 0.0172);Gain of disorder (P = 0.0172);Gain of disorder (P = 0.0172);Gain of disorder (P = 0.0172);
MVP		0.14
MPC		0.54
ClinPred		0.076	T
GERP RS		-6.9
Varity_R		0.054
gMVP		0.17

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs5030878; hg19: chr19-52250216;