rs201182683
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004104.5(FASN):c.3337A>G(p.Ile1113Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000232 in 1,611,900 control chromosomes in the GnomAD database, including 4 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I1113M) has been classified as Uncertain significance.
Frequency
Consequence
NM_004104.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FASN | NM_004104.5 | c.3337A>G | p.Ile1113Val | missense_variant | 21/43 | ENST00000306749.4 | |
FASN | XM_011523538.3 | c.3337A>G | p.Ile1113Val | missense_variant | 21/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.3337A>G | p.Ile1113Val | missense_variant | 21/43 | 1 | NM_004104.5 | P1 | |
FASN | ENST00000634990.1 | c.3337A>G | p.Ile1113Val | missense_variant | 21/43 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000304 AC: 75AN: 246494Hom.: 1 AF XY: 0.000276 AC XY: 37AN XY: 134134
GnomAD4 exome AF: 0.000240 AC: 350AN: 1459634Hom.: 4 Cov.: 33 AF XY: 0.000234 AC XY: 170AN XY: 726042
GnomAD4 genome ? AF: 0.000158 AC: 24AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.000215 AC XY: 16AN XY: 74458
ClinVar
Submissions by phenotype
Epileptic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at