rs12069239
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018994.3(FBXO42):c.1411C>G(p.Pro471Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 1,613,826 control chromosomes in the GnomAD database, including 102,988 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_018994.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBXO42 | NM_018994.3 | c.1411C>G | p.Pro471Ala | missense_variant | 10/10 | ENST00000375592.8 | |
FBXO42 | XM_047422747.1 | c.1411C>G | p.Pro471Ala | missense_variant | 12/12 | ||
FBXO42 | XM_047422750.1 | c.1411C>G | p.Pro471Ala | missense_variant | 12/12 | ||
FBXO42 | XM_047422751.1 | c.1411C>G | p.Pro471Ala | missense_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBXO42 | ENST00000375592.8 | c.1411C>G | p.Pro471Ala | missense_variant | 10/10 | 1 | NM_018994.3 | P1 | |
FBXO42 | ENST00000444116.1 | c.565C>G | p.Pro189Ala | missense_variant | 4/4 | 5 | |||
FBXO42 | ENST00000456164.5 | c.565C>G | p.Pro189Ala | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.354 AC: 53767AN: 151890Hom.: 10024 Cov.: 32
GnomAD3 exomes AF: 0.297 AC: 74578AN: 250894Hom.: 12347 AF XY: 0.293 AC XY: 39841AN XY: 135746
GnomAD4 exome AF: 0.348 AC: 509312AN: 1461818Hom.: 92945 Cov.: 57 AF XY: 0.342 AC XY: 248964AN XY: 727206
GnomAD4 genome ? AF: 0.354 AC: 53823AN: 152008Hom.: 10043 Cov.: 32 AF XY: 0.346 AC XY: 25686AN XY: 74314
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at