chr1-16251126-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018994.3(FBXO42):c.1698G>A(p.Met566Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,614,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018994.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBXO42 | NM_018994.3 | c.1698G>A | p.Met566Ile | missense_variant | 10/10 | ENST00000375592.8 | |
FBXO42 | XM_047422747.1 | c.1698G>A | p.Met566Ile | missense_variant | 12/12 | ||
FBXO42 | XM_047422750.1 | c.1698G>A | p.Met566Ile | missense_variant | 12/12 | ||
FBXO42 | XM_047422751.1 | c.1698G>A | p.Met566Ile | missense_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBXO42 | ENST00000375592.8 | c.1698G>A | p.Met566Ile | missense_variant | 10/10 | 1 | NM_018994.3 | P1 | |
FBXO42 | ENST00000444116.1 | c.852G>A | p.Met284Ile | missense_variant | 4/4 | 5 | |||
FBXO42 | ENST00000456164.5 | c.852G>A | p.Met284Ile | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 250892Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135670
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461838Hom.: 0 Cov.: 30 AF XY: 0.0000261 AC XY: 19AN XY: 727220
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74448
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at