5-151505761-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001447.3(FAT2):c.12854G>A(p.Gly4285Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 1,613,806 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. G4285A) has been classified as Likely benign.
Frequency
Consequence
NM_001447.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAT2 | ENST00000261800.6 | c.12854G>A | p.Gly4285Glu | missense_variant | Exon 24 of 24 | 1 | NM_001447.3 | ENSP00000261800.5 | ||
FAT2 | ENST00000520200.5 | c.3170G>A | p.Gly1057Glu | missense_variant | Exon 11 of 11 | 1 | ENSP00000429678.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250814Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135752
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461512Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727086
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152294Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74462
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at