rs202024354
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_004104.5(FASN):c.5220C>T(p.Gly1740=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000274 in 1,607,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004104.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FASN | NM_004104.5 | c.5220C>T | p.Gly1740= | splice_region_variant, synonymous_variant | 31/43 | ENST00000306749.4 | |
FASN | XM_011523538.3 | c.5220C>T | p.Gly1740= | splice_region_variant, synonymous_variant | 31/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.5220C>T | p.Gly1740= | splice_region_variant, synonymous_variant | 31/43 | 1 | NM_004104.5 | P1 | |
FASN | ENST00000634990.1 | c.5214C>T | p.Gly1738= | splice_region_variant, synonymous_variant | 31/43 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152250Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000257 AC: 6AN: 233366Hom.: 0 AF XY: 0.0000157 AC XY: 2AN XY: 127160
GnomAD4 exome AF: 0.0000213 AC: 31AN: 1454654Hom.: 0 Cov.: 41 AF XY: 0.0000207 AC XY: 15AN XY: 723206
GnomAD4 genome ? AF: 0.0000853 AC: 13AN: 152368Hom.: 0 Cov.: 34 AF XY: 0.0000805 AC XY: 6AN XY: 74518
ClinVar
Submissions by phenotype
Epileptic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at