rs200842352
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004104.5(FASN):c.7192G>T(p.Ala2398Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000184 in 1,605,828 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004104.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FASN | NM_004104.5 | c.7192G>T | p.Ala2398Ser | missense_variant | 42/43 | ENST00000306749.4 | |
FASN | XM_011523538.3 | c.7192G>T | p.Ala2398Ser | missense_variant | 42/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.7192G>T | p.Ala2398Ser | missense_variant | 42/43 | 1 | NM_004104.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000624 AC: 151AN: 241808Hom.: 0 AF XY: 0.000560 AC XY: 74AN XY: 132172
GnomAD4 exome AF: 0.000179 AC: 260AN: 1453490Hom.: 1 Cov.: 37 AF XY: 0.000191 AC XY: 138AN XY: 723330
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152338Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74492
ClinVar
Submissions by phenotype
FASN-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 09, 2020 | 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). - |
Epileptic encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at