chrX-138635469-T-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4BP6_Very_StrongBS2
The NM_004114.5(FGF13):c.589A>C(p.Lys197Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000413 in 1,209,212 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004114.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGF13 | NM_004114.5 | c.589A>C | p.Lys197Gln | missense_variant | 4/5 | ENST00000315930.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGF13 | ENST00000315930.11 | c.589A>C | p.Lys197Gln | missense_variant | 4/5 | 1 | NM_004114.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000241 AC: 27AN: 111993Hom.: 0 Cov.: 24 AF XY: 0.000205 AC XY: 7AN XY: 34147
GnomAD3 exomes AF: 0.0000436 AC: 8AN: 183464Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67908
GnomAD4 exome AF: 0.0000210 AC: 23AN: 1097219Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 6AN XY: 362601
GnomAD4 genome ? AF: 0.000241 AC: 27AN: 111993Hom.: 0 Cov.: 24 AF XY: 0.000205 AC XY: 7AN XY: 34147
ClinVar
Submissions by phenotype
FGF13-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 20, 2023 | 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). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | FGF13: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at