rs2228307
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004104.5(FASN):āc.5662A>Gā(p.Ile1888Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00499 in 1,612,872 control chromosomes in the GnomAD database, including 319 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004104.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FASN | NM_004104.5 | c.5662A>G | p.Ile1888Val | missense_variant | 33/43 | ENST00000306749.4 | |
FASN | XM_011523538.3 | c.5662A>G | p.Ile1888Val | missense_variant | 33/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.5662A>G | p.Ile1888Val | missense_variant | 33/43 | 1 | NM_004104.5 | P1 | |
FASN | ENST00000634990.1 | c.5656A>G | p.Ile1886Val | missense_variant | 33/43 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0262 AC: 3987AN: 152096Hom.: 146 Cov.: 33
GnomAD3 exomes AF: 0.00715 AC: 1789AN: 250062Hom.: 78 AF XY: 0.00516 AC XY: 700AN XY: 135702
GnomAD4 exome AF: 0.00276 AC: 4030AN: 1460658Hom.: 169 Cov.: 36 AF XY: 0.00249 AC XY: 1810AN XY: 726626
GnomAD4 genome ? AF: 0.0264 AC: 4017AN: 152214Hom.: 150 Cov.: 33 AF XY: 0.0254 AC XY: 1891AN XY: 74432
ClinVar
Submissions by phenotype
Epileptic encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at