chr8-43140481-C-CGAGCGGGCGGCGGGCATGAGCGGGCGGCGGGCAT
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152419.3(HGSNAT):c.9_10insCGGCGGGCATGAGCGGGCGGCGGGCATGAGCGGG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000119 in 841,590 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000012 ( 0 hom. )
Consequence
HGSNAT
NM_152419.3 5_prime_UTR
NM_152419.3 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0590
Genes affected
HGSNAT (HGNC:26527): (heparan-alpha-glucosaminide N-acetyltransferase) This gene encodes a lysosomal acetyltransferase, which is one of several enzymes involved in the lysosomal degradation of heparin sulfate. Mutations in this gene are associated with Sanfilippo syndrome C, one type of the lysosomal storage disease mucopolysaccaridosis III, which results from impaired degradation of heparan sulfate. [provided by RefSeq, Jan 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HGSNAT | NM_152419.3 | c.9_10insCGGCGGGCATGAGCGGGCGGCGGGCATGAGCGGG | 5_prime_UTR_variant | 1/18 | ENST00000379644.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HGSNAT | ENST00000379644.9 | c.9_10insCGGCGGGCATGAGCGGGCGGCGGGCATGAGCGGG | 5_prime_UTR_variant | 1/18 | 2 | NM_152419.3 | P3 | ||
HGSNAT | ENST00000520704.1 | upstream_gene_variant | 1 | ||||||
HGSNAT | ENST00000517319.1 | upstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000119 AC: 1AN: 841590Hom.: 0 Cov.: 17 AF XY: 0.00000255 AC XY: 1AN XY: 391408
GnomAD4 exome
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1
AN:
841590
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17
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1
AN XY:
391408
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 18, 2021 | May escape nonsense-mediated mRNA decay and/or be rescued by re-initiation Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
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Name
Calibrated prediction
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.