rs201820102
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM4BP6_Very_StrongBS1BS2
The NM_001099922.3(ALG13):āc.3414A>Cā(p.Ter1138TyrextTer5) variant causes a stop lost change. The variant allele was found at a frequency of 0.00129 in 1,206,161 control chromosomes in the GnomAD database, including 2 homozygotes. There are 483 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.00087 ( 0 hom., 20 hem., cov: 23)
Exomes š: 0.0013 ( 2 hom. 463 hem. )
Consequence
ALG13
NM_001099922.3 stop_lost
NM_001099922.3 stop_lost
Scores
1
4
Clinical Significance
Conservation
PhyloP100: 4.58
Genes affected
ALG13 (HGNC:30881): (ALG13 UDP-N-acetylglucosaminyltransferase subunit) The protein encoded by this gene is a subunit of a bipartite UDP-N-acetylglucosamine transferase. It heterodimerizes with asparagine-linked glycosylation 14 homolog to form a functional UDP-GlcNAc glycosyltransferase that catalyzes the second sugar addition of the highly conserved oligosaccharide precursor in endoplasmic reticulum N-linked glycosylation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
PM4
?
Stoplost variant in NM_001099922.3 Downstream stopcodon found after 1153 codons.
BP6
?
Variant X-111759999-A-C is Benign according to our data. Variant chrX-111759999-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 377466.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111759999-A-C is described in Lovd as [Likely_benign].
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000866 (97/112012) while in subpopulation NFE AF= 0.00152 (81/53243). AF 95% confidence interval is 0.00125. There are 0 homozygotes in gnomad4. There are 20 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
BS2
?
High Hemizygotes in GnomAd4 at 20 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG13 | NM_001099922.3 | c.3414A>C | p.Ter1138TyrextTer5 | stop_lost | 27/27 | ENST00000394780.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG13 | ENST00000394780.8 | c.3414A>C | p.Ter1138TyrextTer5 | stop_lost | 27/27 | 2 | NM_001099922.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000866 AC: 97AN: 111960Hom.: 0 Cov.: 23 AF XY: 0.000586 AC XY: 20AN XY: 34112
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GnomAD3 exomes AF: 0.000645 AC: 113AN: 175314Hom.: 0 AF XY: 0.000598 AC XY: 38AN XY: 63508
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GnomAD4 exome AF: 0.00133 AC: 1457AN: 1094149Hom.: 2 Cov.: 30 AF XY: 0.00129 AC XY: 463AN XY: 359889
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GnomAD4 genome ? AF: 0.000866 AC: 97AN: 112012Hom.: 0 Cov.: 23 AF XY: 0.000585 AC XY: 20AN XY: 34174
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 24, 2021 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
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 | Invitae | Jan 31, 2024 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 21, 2018 | This alteration is classified as 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
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 06, 2023 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
FATHMM_MKL
Pathogenic
D
MutationTaster
Benign
N;N
Vest4
GERP RS
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at