rs374817147
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_024740.2(ALG9):āc.1785T>Cā(p.Tyr595=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,614,158 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000072 ( 0 hom., cov: 32)
Exomes š: 0.000021 ( 0 hom. )
Consequence
ALG9
NM_024740.2 synonymous
NM_024740.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.978
Genes affected
ALG9 (HGNC:15672): (ALG9 alpha-1,2-mannosyltransferase) This gene encodes an alpha-1,2-mannosyltransferase enzyme that functions in lipid-linked oligosaccharide assembly. Mutations in this gene result in congenital disorder of glycosylation type Il. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP7
?
Synonymous conserved (PhyloP=0.978 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG9 | NM_024740.2 | c.1785T>C | p.Tyr595= | synonymous_variant | 15/15 | ENST00000616540.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG9 | ENST00000616540.5 | c.1785T>C | p.Tyr595= | synonymous_variant | 15/15 | 1 | NM_024740.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152204Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249172Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135236
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GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461836Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727214
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GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74492
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Nov 15, 2016 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at