rs867229
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001193306.2(FPR1):c.*196C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 532,714 control chromosomes in the GnomAD database, including 10,452 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.22 ( 5184 hom., cov: 31)
Exomes 𝑓: 0.14 ( 5268 hom. )
Consequence
FPR1
NM_001193306.2 3_prime_UTR
NM_001193306.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.646
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FPR1 | NM_001193306.2 | c.*196C>T | 3_prime_UTR_variant | 3/3 | |||
FPR1 | NM_002029.4 | downstream_gene_variant | ENST00000304748.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FPR1 | ENST00000595042.5 | c.*196C>T | 3_prime_UTR_variant | 3/3 | 2 | P1 | |||
FPR1 | ENST00000304748.5 | downstream_gene_variant | 1 | NM_002029.4 | P1 | ||||
FPR1 | ENST00000594900.2 | downstream_gene_variant | 4 | P1 | |||||
FPR1 | ENST00000600815.2 | downstream_gene_variant | 3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.216 AC: 32664AN: 151460Hom.: 5152 Cov.: 31
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GnomAD4 exome AF: 0.141 AC: 53803AN: 381152Hom.: 5268 Cov.: 4 AF XY: 0.139 AC XY: 27532AN XY: 198742
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GnomAD4 genome ? AF: 0.216 AC: 32752AN: 151562Hom.: 5184 Cov.: 31 AF XY: 0.216 AC XY: 16007AN XY: 73990
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at