rs56717389
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001099922.3(ALG13):c.2812_2835del(p.Pro938_Pro945del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000269 in 37,161 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P933P) has been classified as Likely benign.
Frequency
Consequence
NM_001099922.3 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG13 | NM_001099922.3 | c.2812_2835del | p.Pro938_Pro945del | inframe_deletion | 24/27 | ENST00000394780.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG13 | ENST00000394780.8 | c.2812_2835del | p.Pro938_Pro945del | inframe_deletion | 24/27 | 2 | NM_001099922.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000269 AC: 1AN: 37161Hom.: 0 Cov.: 9 AF XY: 0.000140 AC XY: 1AN XY: 7145
GnomAD4 genome ? AF: 0.0000269 AC: 1AN: 37161Hom.: 0 Cov.: 9 AF XY: 0.000140 AC XY: 1AN XY: 7145
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 36 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2022 | This variant, c.2812_2835del, results in the deletion of 8 amino acid(s) of the ALG13 protein (p.Pro938_Pro945del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with ALG13-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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