rs142210016
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_002029.4(FPR1):c.806G>A(p.Arg269His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000773 in 1,614,112 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R269C) has been classified as Uncertain significance.
Frequency
Consequence
NM_002029.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FPR1 | NM_002029.4 | c.806G>A | p.Arg269His | missense_variant | 2/2 | ENST00000304748.5 | |
FPR1 | NM_001193306.2 | c.806G>A | p.Arg269His | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FPR1 | ENST00000304748.5 | c.806G>A | p.Arg269His | missense_variant | 2/2 | 1 | NM_002029.4 | P1 | |
FPR1 | ENST00000594900.2 | c.806G>A | p.Arg269His | missense_variant | 3/3 | 4 | P1 | ||
FPR1 | ENST00000595042.5 | c.806G>A | p.Arg269His | missense_variant | 3/3 | 2 | P1 | ||
FPR1 | ENST00000600815.2 | c.806G>A | p.Arg269His | missense_variant | 2/2 | 3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00343 AC: 522AN: 152120Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00102 AC: 256AN: 250746Hom.: 2 AF XY: 0.000767 AC XY: 104AN XY: 135530
GnomAD4 exome AF: 0.000495 AC: 723AN: 1461874Hom.: 2 Cov.: 72 AF XY: 0.000418 AC XY: 304AN XY: 727240
GnomAD4 genome AF: 0.00345 AC: 525AN: 152238Hom.: 1 Cov.: 32 AF XY: 0.00326 AC XY: 243AN XY: 74468
ClinVar
Submissions by phenotype
Gingival disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
FPR1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 01, 2024 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at