rs9616204
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_024105.4(ALG12):c.664+12A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 1,613,118 control chromosomes in the GnomAD database, including 39,987 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.24 ( 4864 hom., cov: 34)
Exomes 𝑓: 0.21 ( 35123 hom. )
Consequence
ALG12
NM_024105.4 intron
NM_024105.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.67
Genes affected
ALG12 (HGNC:19358): (ALG12 alpha-1,6-mannosyltransferase) This gene encodes a member of the glycosyltransferase 22 family. The encoded protein catalyzes the addition of the eighth mannose residue in an alpha-1,6 linkage onto the dolichol-PP-oligosaccharide precursor (dolichol-PP-Man(7)GlcNAc(2)) required for protein glycosylation. Mutations in this gene have been associated with congenital disorder of glycosylation type Ig (CDG-Ig)characterized by abnormal N-glycosylation. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BP6
Variant 22-49909882-T-C is Benign according to our data. Variant chr22-49909882-T-C is described in ClinVar as [Benign]. Clinvar id is 96098.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-49909882-T-C is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALG12 | NM_024105.4 | c.664+12A>G | intron_variant | ENST00000330817.11 | NP_077010.1 | |||
ALG12 | XM_017028936.2 | c.664+12A>G | intron_variant | XP_016884425.1 | ||||
ALG12 | XM_017028937.2 | c.664+12A>G | intron_variant | XP_016884426.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALG12 | ENST00000330817.11 | c.664+12A>G | intron_variant | 1 | NM_024105.4 | ENSP00000333813.5 | ||||
ALG12 | ENST00000492791.1 | n.193+12A>G | intron_variant | 3 | ENSP00000417387.1 |
Frequencies
GnomAD3 genomes AF: 0.240 AC: 36527AN: 152076Hom.: 4851 Cov.: 34
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GnomAD3 exomes AF: 0.215 AC: 53814AN: 250762Hom.: 6843 AF XY: 0.225 AC XY: 30474AN XY: 135592
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GnomAD4 exome AF: 0.209 AC: 305606AN: 1460926Hom.: 35123 Cov.: 35 AF XY: 0.216 AC XY: 156686AN XY: 726774
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GnomAD4 genome AF: 0.240 AC: 36574AN: 152192Hom.: 4864 Cov.: 34 AF XY: 0.238 AC XY: 17737AN XY: 74434
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 10, 2012 | - - |
ALG12-congenital disorder of glycosylation Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at