11-92353347-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001367949.2(FAT3):c.1235C>T(p.Ser412Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.058 in 1,613,420 control chromosomes in the GnomAD database, including 3,418 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict 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.
Frequency
Consequence
NM_001367949.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAT3 | NM_001367949.2 | c.1235C>T | p.Ser412Phe | missense_variant | 2/28 | ENST00000525166.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAT3 | ENST00000525166.6 | c.1235C>T | p.Ser412Phe | missense_variant | 2/28 | 5 | NM_001367949.2 | ||
FAT3 | ENST00000409404.6 | c.1235C>T | p.Ser412Phe | missense_variant | 1/25 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0777 AC: 11823AN: 152132Hom.: 652 Cov.: 32
GnomAD3 exomes AF: 0.0462 AC: 11416AN: 247230Hom.: 446 AF XY: 0.0436 AC XY: 5850AN XY: 134168
GnomAD4 exome AF: 0.0560 AC: 81782AN: 1461170Hom.: 2763 Cov.: 32 AF XY: 0.0540 AC XY: 39229AN XY: 726826
GnomAD4 genome ? AF: 0.0776 AC: 11822AN: 152250Hom.: 655 Cov.: 32 AF XY: 0.0748 AC XY: 5569AN XY: 74422
ClinVar
Submissions by phenotype
FAT3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 09, 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at