17-82085630-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004104.5(FASN):c.3974C>T(p.Pro1325Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00174 in 1,596,154 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 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. P1325P) 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 -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FASN | NM_004104.5 | c.3974C>T | p.Pro1325Leu | missense_variant | 23/43 | ENST00000306749.4 | |
FASN | XM_011523538.3 | c.3974C>T | p.Pro1325Leu | missense_variant | 23/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.3974C>T | p.Pro1325Leu | missense_variant | 23/43 | 1 | NM_004104.5 | P1 | |
FASN | ENST00000634990.1 | c.3968C>T | p.Pro1323Leu | missense_variant | 23/43 | 5 | |||
FASN | ENST00000579410.1 | n.31C>T | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00142 AC: 216AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00151 AC: 325AN: 215482Hom.: 1 AF XY: 0.00165 AC XY: 194AN XY: 117496
GnomAD4 exome AF: 0.00178 AC: 2565AN: 1443866Hom.: 9 Cov.: 68 AF XY: 0.00177 AC XY: 1270AN XY: 716920
GnomAD4 genome AF: 0.00142 AC: 216AN: 152288Hom.: 0 Cov.: 33 AF XY: 0.00149 AC XY: 111AN XY: 74468
ClinVar
Submissions by phenotype
FASN-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 22, 2021 | This variant is classified as likely 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 | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at