chr17-82084074-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004104.5(FASN):c.4999C>T(p.Pro1667Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00375 in 1,553,648 control chromosomes in the GnomAD database, including 326 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. P1667P) 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 -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FASN | NM_004104.5 | c.4999C>T | p.Pro1667Ser | missense_variant | 29/43 | ENST00000306749.4 | |
FASN | XM_011523538.3 | c.4999C>T | p.Pro1667Ser | missense_variant | 29/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.4999C>T | p.Pro1667Ser | missense_variant | 29/43 | 1 | NM_004104.5 | P1 | |
FASN | ENST00000634990.1 | c.4993C>T | p.Pro1665Ser | missense_variant | 29/43 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00558 AC: 850AN: 152214Hom.: 59 Cov.: 34
GnomAD3 exomes AF: 0.0124 AC: 1881AN: 151084Hom.: 125 AF XY: 0.0120 AC XY: 977AN XY: 81610
GnomAD4 exome AF: 0.00355 AC: 4970AN: 1401316Hom.: 267 Cov.: 42 AF XY: 0.00366 AC XY: 2536AN XY: 691978
GnomAD4 genome AF: 0.00559 AC: 851AN: 152332Hom.: 59 Cov.: 34 AF XY: 0.00626 AC XY: 466AN XY: 74486
ClinVar
Submissions by phenotype
Epileptic encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at