rs1432862
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_001447.3(FAT2):c.1720C>T(p.Arg574Cys) variant causes a missense change. The variant allele was found at a frequency of 0.503 in 1,613,572 control chromosomes in the GnomAD database, including 207,845 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R574H) has been classified as Likely benign.
Frequency
Consequence
NM_001447.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAT2 | NM_001447.3 | c.1720C>T | p.Arg574Cys | missense_variant | 2/24 | ENST00000261800.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAT2 | ENST00000261800.6 | c.1720C>T | p.Arg574Cys | missense_variant | 2/24 | 1 | NM_001447.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.484 AC: 73489AN: 151866Hom.: 17987 Cov.: 32
GnomAD3 exomes AF: 0.466 AC: 116880AN: 251070Hom.: 28361 AF XY: 0.468 AC XY: 63509AN XY: 135740
GnomAD4 exome AF: 0.505 AC: 738745AN: 1461588Hom.: 189845 Cov.: 60 AF XY: 0.502 AC XY: 364928AN XY: 727088
GnomAD4 genome ? AF: 0.484 AC: 73527AN: 151984Hom.: 18000 Cov.: 32 AF XY: 0.481 AC XY: 35715AN XY: 74286
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
FAT2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 08, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Spinocerebellar ataxia 45 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at