16-5071858-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_019109.5(ALG1):c.9C>T(p.Ala3Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000436 in 1,604,784 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Consequence
ALG1
NM_019109.5 synonymous
NM_019109.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.09
Genes affected
ALG1 (HGNC:18294): (ALG1 chitobiosyldiphosphodolichol beta-mannosyltransferase) The enzyme encoded by this gene catalyzes the first mannosylation step in the biosynthesis of lipid-linked oligosaccharides. This gene is mutated in congenital disorder of glycosylation type Ik. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
Variant 16-5071858-C-T is Benign according to our data. Variant chr16-5071858-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2789265.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.09 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALG1 | NM_019109.5 | c.9C>T | p.Ala3Ala | synonymous_variant | 1/13 | ENST00000262374.10 | NP_061982.3 | |
ALG1 | XM_017023457.3 | c.9C>T | p.Ala3Ala | synonymous_variant | 1/12 | XP_016878946.1 | ||
ALG1 | XR_007064892.1 | n.16C>T | non_coding_transcript_exon_variant | 1/10 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152266Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000429 AC: 1AN: 232894Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 127828
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GnomAD4 exome AF: 0.00000413 AC: 6AN: 1452400Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 722704
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GnomAD4 genome AF: 0.00000656 AC: 1AN: 152384Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74522
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
ALG1-congenital disorder of glycosylation Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 26, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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