11-92352457-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001367949.2(FAT3):c.345C>T(p.Ala115Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00421 in 1,612,444 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001367949.2 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAT3 | NM_001367949.2 | c.345C>T | p.Ala115Ala | synonymous_variant | Exon 2 of 28 | ENST00000525166.6 | NP_001354878.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAT3 | ENST00000525166.6 | c.345C>T | p.Ala115Ala | synonymous_variant | Exon 2 of 28 | 5 | NM_001367949.2 | ENSP00000432586.2 | ||
FAT3 | ENST00000409404.6 | c.345C>T | p.Ala115Ala | synonymous_variant | Exon 1 of 25 | 5 | ENSP00000387040.2 |
Frequencies
GnomAD3 genomes AF: 0.00323 AC: 491AN: 152082Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00278 AC: 692AN: 248612Hom.: 2 AF XY: 0.00276 AC XY: 372AN XY: 134884
GnomAD4 exome AF: 0.00431 AC: 6293AN: 1460244Hom.: 20 Cov.: 31 AF XY: 0.00412 AC XY: 2996AN XY: 726424
GnomAD4 genome AF: 0.00323 AC: 491AN: 152200Hom.: 2 Cov.: 32 AF XY: 0.00318 AC XY: 237AN XY: 74432
ClinVar
Submissions by phenotype
FAT3-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
FAT3: BP4, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at