chr17-82091484-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_004104.5(FASN):c.1230G>A(p.Pro410=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000111 in 1,604,302 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. P410P) has been classified as Likely benign.
Frequency
Consequence
NM_004104.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FASN | NM_004104.5 | c.1230G>A | p.Pro410= | synonymous_variant | 9/43 | ENST00000306749.4 | |
FASN | XM_011523538.3 | c.1230G>A | p.Pro410= | synonymous_variant | 9/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.1230G>A | p.Pro410= | synonymous_variant | 9/43 | 1 | NM_004104.5 | P1 | |
FASN | ENST00000634990.1 | c.1230G>A | p.Pro410= | synonymous_variant | 9/43 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152066Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000295 AC: 66AN: 223716Hom.: 0 AF XY: 0.000262 AC XY: 32AN XY: 122354
GnomAD4 exome AF: 0.0000999 AC: 145AN: 1452118Hom.: 0 Cov.: 35 AF XY: 0.0000790 AC XY: 57AN XY: 721804
GnomAD4 genome AF: 0.000217 AC: 33AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74388
ClinVar
Submissions by phenotype
FASN-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 09, 2019 | 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 | Dec 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at