19-51745957-CT-TG

Variant names:

• chr19-51745957-CT-TG
• rs1555796329
• NM_002029.4:c.1037_1038delAGinsCA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The NM_002029.4(FPR1):​c.1037_1038delAGinsCA​(p.Glu346Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Benign in ClinVar. Synonymous variant affecting the same amino acid position (i.e. E346E) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 30)
• Consequence: FPR1 NM_002029.4 missense
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.10

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
• BP6: Variant 19-51745957-CT-TG is Benign according to our data. Variant chr19-51745957-CT-TG is described in ClinVar as [Benign]. Clinvar id is 526513.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FPR1	NM_002029.4	c.1037_1038delAGinsCA	p.Glu346Ala	missense_variant		ENST00000304748.5	NP_002020.1
FPR1	NM_001193306.2	c.1037_1038delAGinsCA	p.Glu346Ala	missense_variant			NP_001180235.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FPR1	ENST00000304748.5	c.1037_1038delAGinsCA	p.Glu346Ala	missense_variant		1	NM_002029.4	ENSP00000302707.3
FPR1	ENST00000594900.2	c.1037_1038delAGinsCA	p.Glu346Ala	missense_variant		4		ENSP00000470750.2
FPR1	ENST00000595042.5	c.1037_1038delAGinsCA	p.Glu346Ala	missense_variant		2		ENSP00000471493.1
FPR1	ENST00000600815.2	c.1037_1038delAGinsCA	p.Glu346Ala	missense_variant		3		ENSP00000472936.2

Frequencies

GnomAD3 genomes Cov.: 30

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 30

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Gingival disorder Benign:1

Dec 30, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555796329; hg19: chr19-52249210;