rs5030879
Positions:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_002029.4(FPR1):c.348C>T(p.Ile116=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0205 in 1,614,018 control chromosomes in the GnomAD database, including 3,791 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.090 ( 1929 hom., cov: 32)
Exomes 𝑓: 0.013 ( 1862 hom. )
Consequence
FPR1
NM_002029.4 synonymous
NM_002029.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.08
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
Variant 19-51746647-G-A is Benign according to our data. Variant chr19-51746647-G-A is described in ClinVar as [Benign]. Clinvar id is 456366.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.08 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FPR1 | NM_002029.4 | c.348C>T | p.Ile116= | synonymous_variant | 2/2 | ENST00000304748.5 | |
FPR1 | NM_001193306.2 | c.348C>T | p.Ile116= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FPR1 | ENST00000304748.5 | c.348C>T | p.Ile116= | synonymous_variant | 2/2 | 1 | NM_002029.4 | P1 | |
FPR1 | ENST00000594900.2 | c.348C>T | p.Ile116= | synonymous_variant | 3/3 | 4 | P1 | ||
FPR1 | ENST00000595042.5 | c.348C>T | p.Ile116= | synonymous_variant | 3/3 | 2 | P1 | ||
FPR1 | ENST00000600815.2 | c.348C>T | p.Ile116= | synonymous_variant | 2/2 | 3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0896 AC: 13620AN: 152010Hom.: 1925 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
13620
AN:
152010
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0285 AC: 7157AN: 251290Hom.: 806 AF XY: 0.0228 AC XY: 3090AN XY: 135816
GnomAD3 exomes
AF:
AC:
7157
AN:
251290
Hom.:
AF XY:
AC XY:
3090
AN XY:
135816
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0132 AC: 19360AN: 1461890Hom.: 1862 Cov.: 76 AF XY: 0.0124 AC XY: 9018AN XY: 727246
GnomAD4 exome
AF:
AC:
19360
AN:
1461890
Hom.:
Cov.:
76
AF XY:
AC XY:
9018
AN XY:
727246
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0898 AC: 13661AN: 152128Hom.: 1929 Cov.: 32 AF XY: 0.0868 AC XY: 6458AN XY: 74380
GnomAD4 genome
?
AF:
AC:
13661
AN:
152128
Hom.:
Cov.:
32
AF XY:
AC XY:
6458
AN XY:
74380
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
170
AN:
3478
EpiCase
AF:
EpiControl
AF:
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 submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at