19-51745957-CT-TG

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_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 (★).

Frequency

Genomes: not found (cov: 30)

Consequence

FPR1
NM_002029.4 missense

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.10
Variant links:
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]

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ACMG classification

Classification made for transcript

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/exons MANE Protein UniProt
FPR1NM_002029.4 linkuse as main transcriptc.1037_1038delAGinsCA p.Glu346Ala missense_variant ENST00000304748.5 NP_002020.1 P21462
FPR1NM_001193306.2 linkuse as main transcriptc.1037_1038delAGinsCA p.Glu346Ala missense_variant NP_001180235.1 P21462

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FPR1ENST00000304748.5 linkuse as main transcriptc.1037_1038delAGinsCA p.Glu346Ala missense_variant 1 NM_002029.4 ENSP00000302707.3 P21462
FPR1ENST00000594900.2 linkuse as main transcriptc.1037_1038delAGinsCA p.Glu346Ala missense_variant 4 ENSP00000470750.2 P21462M0QZT0
FPR1ENST00000595042.5 linkuse as main transcriptc.1037_1038delAGinsCA p.Glu346Ala missense_variant 2 ENSP00000471493.1 P21462
FPR1ENST00000600815.2 linkuse as main transcriptc.1037_1038delAGinsCA p.Glu346Ala missense_variant 3 ENSP00000472936.2 P21462M0R315

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
LINK: link

Submissions by phenotype

Gingival disorder Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 19, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1555796329; hg19: chr19-52249210; API