rs201335279
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP2
The NM_001447.3(FAT2):c.10946G>A(p.Arg3649Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000105 in 1,613,924 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R3649W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001447.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAT2 | NM_001447.3 | c.10946G>A | p.Arg3649Gln | missense_variant | 19/24 | ENST00000261800.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAT2 | ENST00000261800.6 | c.10946G>A | p.Arg3649Gln | missense_variant | 19/24 | 1 | NM_001447.3 | P1 | |
FAT2 | ENST00000520200.5 | c.1523G>A | p.Arg508Gln | missense_variant | 6/11 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000800 AC: 2AN: 249918Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135386
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461738Hom.: 0 Cov.: 85 AF XY: 0.0000138 AC XY: 10AN XY: 727182
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152186Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74336
ClinVar
Submissions by phenotype
Spinocerebellar ataxia 45 Pathogenic:1Uncertain:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 16, 2017 | - - |
Uncertain significance, criteria provided, single submitter | curation | SIB Swiss Institute of Bioinformatics | Oct 15, 2018 | This variant is interpreted as Uncertain Significance - Insufficient Evidence, for Spinocerebellar ataxia 45, autosomal dominant. The following ACMG Tag(s) were applied: PM2-Supporting => PM2 downgraded in strength to Supporting. PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product (https://www.ncbi.nlm.nih.gov/pubmed/29053796). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at