rs1057344564
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004104.5(FASN):āc.6563A>Gā(p.Gln2188Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000314 in 1,594,710 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (ā ).
Frequency
Consequence
NM_004104.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FASN | NM_004104.5 | c.6563A>G | p.Gln2188Arg | missense_variant | 38/43 | ENST00000306749.4 | NP_004095.4 | |
FASN | XM_011523538.3 | c.6563A>G | p.Gln2188Arg | missense_variant | 38/43 | XP_011521840.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FASN | ENST00000306749.4 | c.6563A>G | p.Gln2188Arg | missense_variant | 38/43 | 1 | NM_004104.5 | ENSP00000304592.2 | ||
FASN | ENST00000634990.1 | c.6557A>G | p.Gln2186Arg | missense_variant | 38/43 | 5 | ENSP00000488964.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000229 AC: 5AN: 217962Hom.: 0 AF XY: 0.0000169 AC XY: 2AN XY: 118276
GnomAD4 exome AF: 0.0000291 AC: 42AN: 1442480Hom.: 0 Cov.: 36 AF XY: 0.0000335 AC XY: 24AN XY: 715832
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74370
ClinVar
Submissions by phenotype
Epileptic encephalopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 12, 2021 | This sequence change replaces glutamine with arginine at codon 2188 of the FASN protein (p.Gln2188Arg). The glutamine residue is moderately conserved and there is a small physicochemical difference between glutamine and arginine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with FASN-related conditions. ClinVar contains an entry for this variant (Variation ID: 581409). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at