rs142611552

Variant names:

• chr19-51768827-C-G
• rs142611552
• NM_001005738.2:c.169C>G

Your query was ambiguous. Multiple possible variants found:

• chr19-51768827-C-G
• chr19-51768827-C-T

Variant summary

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

The NM_001005738.2(FPR2):​c.169C>G​(p.Arg57Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,894 control chromosomes in the GnomAD database, including 1 homozygotes. 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. R57C) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (1 hom.)
• Consequence: FPR2 NM_001005738.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.16

Genes affected

FPR2 (HGNC:3827): (formyl peptide receptor 2) Enables amyloid-beta binding activity; scavenger receptor binding activity; and signaling receptor activity. Involved in several processes, including cellular response to amyloid-beta; positive regulation of monocyte chemotaxis; and regulation of defense response. Located in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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 rank	MANE	Protein	UniProt
FPR2	NM_001005738.2	c.169C>G	p.Arg57Gly	missense_variant	Exon 2 of 2	ENST00000340023.7	NP_001005738.1
FPR2	NM_001462.3	c.169C>G	p.Arg57Gly	missense_variant	Exon 2 of 2		NP_001453.1
FPR2	XM_006723120.4	c.169C>G	p.Arg57Gly	missense_variant	Exon 3 of 3		XP_006723183.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FPR2	ENST00000340023.7	c.169C>G	p.Arg57Gly	missense_variant	Exon 2 of 2	1	NM_001005738.2	ENSP00000340191.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000795 AC: 2 AN: 251478 Hom.: 1 AF XY: 0.0000147 AC XY: 2 AN XY: 135908

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000653

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461894 Hom.: 1 Cov.: 31 AF XY: 0.00000275 AC XY: 2 AN XY: 727248

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000232

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.33
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.34
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.41	.;T;.;T;T;.
Eigen	Uncertain	0.52
Eigen_PC	Uncertain	0.42
FATHMM_MKL	Uncertain	0.79	D
LIST_S2	Benign	0.23	T;.;T;.;T;T
M_CAP	Benign	0.0050	T
MetaRNN	Uncertain	0.69	D;D;D;D;D;D
MetaSVM	Benign	-0.80	T
MutationAssessor	Pathogenic	3.1	.;M;.;M;M;.
PrimateAI	Benign	0.28	T
PROVEAN	Pathogenic	-4.5	.;D;.;.;.;.
REVEL	Benign	0.21
Sift	Uncertain	0.010	.;D;.;.;.;.
Sift4G	Benign	0.093	T;D;T;D;D;D
Polyphen		0.90	.;P;.;P;P;.
Vest4		0.075, 0.084
MutPred		0.75		Loss of MoRF binding (P = 0.0493);Loss of MoRF binding (P = 0.0493);Loss of MoRF binding (P = 0.0493);Loss of MoRF binding (P = 0.0493);Loss of MoRF binding (P = 0.0493);Loss of MoRF binding (P = 0.0493);
MVP		0.69
MPC		0.54
ClinPred		0.92	D
GERP RS		3.6
Varity_R		0.36
gMVP		0.50

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: rs142611552; hg19: chr19-52272080;