19-51745957-CT-TG

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. 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. The variant is present in control chromosomes in GnomAd MNV project. The variant allele was found at a frequency of 0.00022 in 62 alleles, including 0 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. 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: GnomAD MNV: 𝑓 0.00022 Genomes: not found (cov: 30)
• Consequence: FPR1 NM_002029.4 missense
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.10
• Publications: 0 publications found

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]

FPR1 Gene-Disease associations (from GenCC):

• susceptibility to localized juvenile periodontitis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -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 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

GnomAD MNV AF: 0.000220 AC: 62 Hom.: 0

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

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1555796329; hg19: chr19-52249210;