rs2070745
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002029.4(FPR1):āc.301G>Cā(p.Val101Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 1,613,728 control chromosomes in the GnomAD database, including 114,578 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V101I) 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 -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FPR1 | NM_002029.4 | c.301G>C | p.Val101Leu | missense_variant | 2/2 | ENST00000304748.5 | |
FPR1 | NM_001193306.2 | c.301G>C | p.Val101Leu | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FPR1 | ENST00000304748.5 | c.301G>C | p.Val101Leu | missense_variant | 2/2 | 1 | NM_002029.4 | P1 | |
FPR1 | ENST00000594900.2 | c.301G>C | p.Val101Leu | missense_variant | 3/3 | 4 | P1 | ||
FPR1 | ENST00000595042.5 | c.301G>C | p.Val101Leu | missense_variant | 3/3 | 2 | P1 | ||
FPR1 | ENST00000600815.2 | c.301G>C | p.Val101Leu | missense_variant | 2/2 | 3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.370 AC: 56191AN: 151790Hom.: 10667 Cov.: 31
GnomAD3 exomes AF: 0.401 AC: 100695AN: 251342Hom.: 21697 AF XY: 0.390 AC XY: 52939AN XY: 135840
GnomAD4 exome AF: 0.372 AC: 544174AN: 1461820Hom.: 103905 Cov.: 76 AF XY: 0.370 AC XY: 269277AN XY: 727210
GnomAD4 genome ? AF: 0.370 AC: 56221AN: 151908Hom.: 10673 Cov.: 31 AF XY: 0.375 AC XY: 27859AN XY: 74258
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: MAF - |
Gingival disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Other:1
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at