rs72914988
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001291303.3(FAT4):c.7358G>T(p.Ser2453Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00129 in 1,613,542 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001291303.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAT4 | NM_001291303.3 | c.7358G>T | p.Ser2453Ile | missense_variant | 9/18 | ENST00000394329.9 | NP_001278232.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAT4 | ENST00000394329.9 | c.7358G>T | p.Ser2453Ile | missense_variant | 9/18 | 5 | NM_001291303.3 | ENSP00000377862 | P1 | |
FAT4 | ENST00000335110.5 | c.2246G>T | p.Ser749Ile | missense_variant | 8/15 | 1 | ENSP00000335169 | |||
FAT4 | ENST00000674496.2 | c.2129G>T | p.Ser710Ile | missense_variant | 8/17 | ENSP00000501473 | ||||
FAT4 | ENST00000509444.1 | n.341G>T | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00319 AC: 485AN: 152072Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00167 AC: 419AN: 250898Hom.: 3 AF XY: 0.00141 AC XY: 191AN XY: 135580
GnomAD4 exome AF: 0.00109 AC: 1592AN: 1461352Hom.: 7 Cov.: 31 AF XY: 0.00105 AC XY: 760AN XY: 726990
GnomAD4 genome AF: 0.00319 AC: 485AN: 152190Hom.: 4 Cov.: 32 AF XY: 0.00331 AC XY: 246AN XY: 74416
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 26, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 16, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2024 | FAT4: BP4, BS2 - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 14, 2016 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 25, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
FAT4-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 04, 2020 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at