chrX-111708022-C-T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_001099922.3(ALG13):c.384-5C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000712 in 1,194,243 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 17 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001099922.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG13 | NM_001099922.3 | c.384-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000394780.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG13 | ENST00000394780.8 | c.384-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | NM_001099922.3 | A2 | |||
ALG13-AS1 | ENST00000430794.1 | n.107-1285G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 11AN: 111605Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33779
GnomAD3 exomes AF: 0.000318 AC: 51AN: 160480Hom.: 0 AF XY: 0.000197 AC XY: 10AN XY: 50746
GnomAD4 exome AF: 0.0000684 AC: 74AN: 1082583Hom.: 0 Cov.: 31 AF XY: 0.0000483 AC XY: 17AN XY: 351821
GnomAD4 genome AF: 0.0000985 AC: 11AN: 111660Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33844
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 36 Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2017 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
ALG13-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | 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 | GeneDx | Apr 20, 2020 | This variant is associated with the following publications: (PMID: 29314583) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at