4-125317769-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_StrongBS1
The NM_001291303.3(FAT4):c.1358A>G(p.Gln453Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. Q453L) has been classified as Benign.
Frequency
Consequence
NM_001291303.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAT4 | NM_001291303.3 | c.1358A>G | p.Gln453Arg | missense_variant | 2/18 | ENST00000394329.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAT4 | ENST00000394329.9 | c.1358A>G | p.Gln453Arg | missense_variant | 2/18 | 5 | NM_001291303.3 | P1 | |
FAT4 | ENST00000674496.2 | c.-55+1792A>G | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 151990Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249260Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135286
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461828Hom.: 0 Cov.: 71 AF XY: 0.00000275 AC XY: 2AN XY: 727208
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 151990Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74216
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at