rs1042229
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002029.4(FPR1):āc.576T>Gā(p.Asn192Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 1,613,830 control chromosomes in the GnomAD database, including 91,883 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 (ā ā ). Synonymous variant affecting the same amino acid position (i.e. N192N) has been classified as Benign.
Frequency
Consequence
NM_002029.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FPR1 | NM_002029.4 | c.576T>G | p.Asn192Lys | missense_variant | 2/2 | ENST00000304748.5 | |
FPR1 | NM_001193306.2 | c.576T>G | p.Asn192Lys | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FPR1 | ENST00000304748.5 | c.576T>G | p.Asn192Lys | missense_variant | 2/2 | 1 | NM_002029.4 | P1 | |
FPR1 | ENST00000594900.2 | c.576T>G | p.Asn192Lys | missense_variant | 3/3 | 4 | P1 | ||
FPR1 | ENST00000595042.5 | c.576T>G | p.Asn192Lys | missense_variant | 3/3 | 2 | P1 | ||
FPR1 | ENST00000600815.2 | c.576T>G | p.Asn192Lys | missense_variant | 2/2 | 3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.362 AC: 54938AN: 151860Hom.: 10298 Cov.: 31
GnomAD3 exomes AF: 0.319 AC: 80159AN: 251308Hom.: 13345 AF XY: 0.321 AC XY: 43583AN XY: 135826
GnomAD4 exome AF: 0.331 AC: 484143AN: 1461852Hom.: 81572 Cov.: 70 AF XY: 0.331 AC XY: 241038AN XY: 727238
GnomAD4 genome AF: 0.362 AC: 54982AN: 151978Hom.: 10311 Cov.: 31 AF XY: 0.359 AC XY: 26692AN XY: 74300
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Gingival disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 29, 2020 | This variant is associated with the following publications: (PMID: 12595898) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at