17-82081851-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004104.5(FASN):c.6164-8C>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00416 in 1,599,194 control chromosomes in the GnomAD database, including 241 homozygotes. 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 Benign (★★).
Frequency
Consequence
NM_004104.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FASN | NM_004104.5 | c.6164-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000306749.4 | |||
FASN | XM_011523538.3 | c.6164-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.6164-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004104.5 | P1 | |||
FASN | ENST00000634990.1 | c.6158-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0218 AC: 3284AN: 150916Hom.: 115 Cov.: 30
GnomAD3 exomes AF: 0.00553 AC: 1265AN: 228900Hom.: 43 AF XY: 0.00425 AC XY: 540AN XY: 126916
GnomAD4 exome AF: 0.00231 AC: 3340AN: 1448158Hom.: 123 Cov.: 42 AF XY: 0.00201 AC XY: 1444AN XY: 719894
GnomAD4 genome AF: 0.0219 AC: 3309AN: 151036Hom.: 118 Cov.: 30 AF XY: 0.0213 AC XY: 1575AN XY: 73780
ClinVar
Submissions by phenotype
FASN-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 09, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
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