rs1555796329

chr19-51745957-CT-TG

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_002029.4(FPR1):c.1037_1038delinsCA(p.Glu346Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Benignin 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 Likely_benign. Variant got -2 ACMG points.

• 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/exons	MANE	UniProt
FPR1	NM_002029.4	c.1037_1038delinsCA	p.Glu346Ala	missense_variant	2/2	ENST00000304748.5
FPR1	NM_001193306.2	c.1037_1038delinsCA	p.Glu346Ala	missense_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FPR1	ENST00000304748.5	c.1037_1038delinsCA	p.Glu346Ala	missense_variant	2/2	1	NM_002029.4	P1
FPR1	ENST00000594900.2	c.1037_1038delinsCA	p.Glu346Ala	missense_variant	3/3	4		P1
FPR1	ENST00000595042.5	c.1037_1038delinsCA	p.Glu346Ala	missense_variant	3/3	2		P1
FPR1	ENST00000600815.2	c.1037_1038delinsCA	p.Glu346Ala	missense_variant	2/2	3		P1

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

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 19, 2024

- -

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;