rs199546508
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PP3_StrongBS2
The NM_004104.5(FASN):c.2593G>A(p.Asp865Asn) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000459 in 1,612,178 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004104.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FASN | NM_004104.5 | c.2593G>A | p.Asp865Asn | missense_variant, splice_region_variant | Exon 16 of 43 | ENST00000306749.4 | NP_004095.4 | |
FASN | XM_011523538.3 | c.2593G>A | p.Asp865Asn | missense_variant, splice_region_variant | Exon 16 of 43 | XP_011521840.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.2593G>A | p.Asp865Asn | missense_variant, splice_region_variant | Exon 16 of 43 | 1 | NM_004104.5 | ENSP00000304592.2 | ||
FASN | ENST00000634990.1 | c.2593G>A | p.Asp865Asn | missense_variant, splice_region_variant | Exon 16 of 43 | 5 | ENSP00000488964.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152126Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000606 AC: 15AN: 247668Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134916
GnomAD4 exome AF: 0.0000459 AC: 67AN: 1459934Hom.: 0 Cov.: 35 AF XY: 0.0000468 AC XY: 34AN XY: 726198
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74444
ClinVar
Submissions by phenotype
Epileptic encephalopathy Uncertain:1
This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 865 of the FASN protein (p.Asp865Asn). This variant also falls at the last nucleotide of exon 16, which is part of the consensus splice site for this exon. This variant is present in population databases (rs199546508, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with FASN-related conditions. ClinVar contains an entry for this variant (Variation ID: 462025). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at