5-150521293-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001543.5(NDST1):āc.39C>Gā(p.His13Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,612,262 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
NM_001543.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249422Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135082
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460124Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726494
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74306
ClinVar
Submissions by phenotype
not provided Uncertain:1
Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge -
Intellectual disability, autosomal recessive 46 Uncertain:1
This 5-year old male with a history of global developmental delay, hyperkinesis, and mixed receptive-expressive language disorder was found to be compound heterozygous for two variants in the NDST1 gene. This particular variant has been reported in the non-Finnish European population at a frequency of 0.0009%. Computational models are inconsistent. This variant is not in either the heparan sulfate N-deacetylase 1 domain or the sulfotransferase domain. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at