X-111744768-ACCTCCTCCTCCTCCTCCTCCTCCT-ACCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001099922.3(ALG13):c.2827_2835dupCCTCCTCCT(p.Pro943_Pro945dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000404 in 594,504 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., 0 hem., cov: 18)
Exomes 𝑓: 0.000036 ( 0 hom. 5 hem. )
Consequence
ALG13
NM_001099922.3 conservative_inframe_insertion
NM_001099922.3 conservative_inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.159
Genes affected
ALG13 (HGNC:30881): (ALG13 UDP-N-acetylglucosaminyltransferase subunit) The protein encoded by this gene is a subunit of a bipartite UDP-N-acetylglucosamine transferase. It heterodimerizes with asparagine-linked glycosylation 14 homolog to form a functional UDP-GlcNAc glycosyltransferase that catalyzes the second sugar addition of the highly conserved oligosaccharide precursor in endoplasmic reticulum N-linked glycosylation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
Variant X-111744768-A-ACCTCCTCCT is Benign according to our data. Variant chrX-111744768-A-ACCTCCTCCT is described in ClinVar as [Likely_benign]. Clinvar id is 1593273.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Hemizygotes in GnomAdExome4 at 5 XL gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000108 AC: 4AN: 37159Hom.: 0 Cov.: 18 AF XY: 0.00 AC XY: 0AN XY: 7145
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GnomAD4 exome AF: 0.0000359 AC: 20AN: 557345Hom.: 0 Cov.: 24 AF XY: 0.0000315 AC XY: 5AN XY: 158541
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GnomAD4 genome AF: 0.000108 AC: 4AN: 37159Hom.: 0 Cov.: 18 AF XY: 0.00 AC XY: 0AN XY: 7145
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Developmental and epileptic encephalopathy, 36 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 28, 2023 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at