chr17-82081633-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004104.5(FASN):c.6374G>A(p.Arg2125Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00504 in 1,612,718 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2125W) 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.6374G>A | p.Arg2125Gln | missense_variant | 37/43 | ENST00000306749.4 | |
FASN | XM_011523538.3 | c.6374G>A | p.Arg2125Gln | missense_variant | 37/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.6374G>A | p.Arg2125Gln | missense_variant | 37/43 | 1 | NM_004104.5 | P1 | |
FASN | ENST00000634990.1 | c.6368G>A | p.Arg2123Gln | missense_variant | 37/43 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00346 AC: 526AN: 152170Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.00313 AC: 780AN: 249042Hom.: 3 AF XY: 0.00305 AC XY: 413AN XY: 135440
GnomAD4 exome AF: 0.00520 AC: 7600AN: 1460430Hom.: 26 Cov.: 42 AF XY: 0.00499 AC XY: 3623AN XY: 726512
GnomAD4 genome AF: 0.00346 AC: 527AN: 152288Hom.: 1 Cov.: 31 AF XY: 0.00290 AC XY: 216AN XY: 74470
ClinVar
Submissions by phenotype
Epileptic encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | FASN: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at