rs148372886
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004104.5(FASN):c.7357G>A(p.Ala2453Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000446 in 1,612,988 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★). Synonymous variant affecting the same amino acid position (i.e. A2453A) has been classified as Likely benign.
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.7357G>A | p.Ala2453Thr | missense_variant | 42/43 | ENST00000306749.4 | |
FASN | XM_011523538.3 | c.7357G>A | p.Ala2453Thr | missense_variant | 42/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.7357G>A | p.Ala2453Thr | missense_variant | 42/43 | 1 | NM_004104.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152264Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000641 AC: 16AN: 249694Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135540
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1460606Hom.: 0 Cov.: 37 AF XY: 0.0000317 AC XY: 23AN XY: 726612
GnomAD4 genome AF: 0.000184 AC: 28AN: 152382Hom.: 0 Cov.: 33 AF XY: 0.000174 AC XY: 13AN XY: 74512
ClinVar
Submissions by phenotype
Epileptic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 17, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at