chr11-111783896-CTATAT-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_024740.2(ALG9):c.*2496_*2500delATATA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.26 ( 5296 hom., cov: 19)
Failed GnomAD Quality Control
Consequence
ALG9
NM_024740.2 3_prime_UTR
NM_024740.2 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.28
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 Benign. Variant got -10 ACMG points.
BP6
Variant 11-111783896-CTATAT-C is Benign according to our data. Variant chr11-111783896-CTATAT-C is described in ClinVar as [Likely_benign]. Clinvar id is 302379.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.262 AC: 38960AN: 148562Hom.: 5297 Cov.: 19
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.262 AC: 38965AN: 148666Hom.: 5296 Cov.: 19 AF XY: 0.262 AC XY: 18965AN XY: 72348
GnomAD4 genome
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18965
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Asia WGS
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729
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3450
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital disorder of glycosylation Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at