rs61744789
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_033087.4(ALG2):āc.84C>Gā(p.Gly28=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00244 in 1,597,644 control chromosomes in the GnomAD database, including 80 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.0034 ( 11 hom., cov: 33)
Exomes š: 0.0023 ( 69 hom. )
Consequence
ALG2
NM_033087.4 synonymous
NM_033087.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0440
Genes affected
ALG2 (HGNC:23159): (ALG2 alpha-1,3/1,6-mannosyltransferase) This gene encodes a member of the glycosyltransferase 1 family. The encoded protein acts as an alpha 1,3 mannosyltransferase, mannosylating Man(2)GlcNAc(2)-dolichol diphosphate and Man(1)GlcNAc(2)-dolichol diphosphate to form Man(3)GlcNAc(2)-dolichol diphosphate. Defects in this gene have been associated with congenital disorder of glycosylation type Ih (CDG-Ii). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 9-99221811-G-C is Benign according to our data. Variant chr9-99221811-G-C is described in ClinVar as [Benign]. Clinvar id is 193473.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.044 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0538 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG2 | NM_033087.4 | c.84C>G | p.Gly28= | synonymous_variant | 1/2 | ENST00000476832.2 | |
ALG2 | NR_024532.2 | n.132C>G | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG2 | ENST00000476832.2 | c.84C>G | p.Gly28= | synonymous_variant | 1/2 | 1 | NM_033087.4 | P1 | |
ALG2 | ENST00000238477.5 | c.84C>G | p.Gly28= | synonymous_variant, NMD_transcript_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00346 AC: 526AN: 152242Hom.: 11 Cov.: 33
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GnomAD3 exomes AF: 0.00885 AC: 1987AN: 224464Hom.: 40 AF XY: 0.00709 AC XY: 882AN XY: 124482
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GnomAD4 exome AF: 0.00233 AC: 3370AN: 1445284Hom.: 69 Cov.: 32 AF XY: 0.00211 AC XY: 1515AN XY: 719426
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GnomAD4 genome ? AF: 0.00344 AC: 524AN: 152360Hom.: 11 Cov.: 33 AF XY: 0.00376 AC XY: 280AN XY: 74508
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 14, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 09, 2015 | - - |
ALG2-congenital disorder of glycosylation;C4015597:Congenital myasthenic syndrome 14 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at