chrX-138739247-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The ENST00000305414.9(FGF13):āc.23A>Gā(p.Tyr8Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000595 in 1,125,283 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 170 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 9/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
ENST00000305414.9 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 |
---|---|---|---|---|---|---|---|
FGF13 | NM_033642.3 | c.23A>G | p.Tyr8Cys | missense_variant | 1/5 | ||
FGF13 | NM_001139498.2 | c.50-30319A>G | intron_variant | ||||
FGF13 | NM_001139500.2 | c.218-30319A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGF13 | ENST00000305414.9 | c.23A>G | p.Tyr8Cys | missense_variant | 1/5 | 1 | |||
FGF13 | ENST00000436198.6 | c.218-30319A>G | intron_variant | 2 | A1 | ||||
FGF13 | ENST00000441825.8 | c.131-30319A>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 31AN: 112201Hom.: 0 Cov.: 23 AF XY: 0.000291 AC XY: 10AN XY: 34363
GnomAD3 exomes AF: 0.000370 AC: 65AN: 175674Hom.: 0 AF XY: 0.000311 AC XY: 19AN XY: 61040
GnomAD4 exome AF: 0.000631 AC: 639AN: 1013082Hom.: 0 Cov.: 19 AF XY: 0.000525 AC XY: 160AN XY: 304964
GnomAD4 genome AF: 0.000276 AC: 31AN: 112201Hom.: 0 Cov.: 23 AF XY: 0.000291 AC XY: 10AN XY: 34363
ClinVar
Submissions by phenotype
FGF13-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 08, 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 | Jan 01, 2024 | FGF13: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at