rs201629807
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_001543.5(NDST1):c.1314C>T(p.Pro438=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000148 in 1,614,202 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 0.00015 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00015 ( 0 hom. )
Consequence
NDST1
NM_001543.5 synonymous
NM_001543.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.59
Genes affected
NDST1 (HGNC:7680): (N-deacetylase and N-sulfotransferase 1) This gene encodes a member of the heparan sulfate/heparin GlcNAc N-deacetylase/ N-sulfotransferase family. The encoded enzyme is a type II transmembrane protein that resides in the Golgi apparatus. The encoded protein catalyzes the transfer of sulfate from 3'-phosphoadenosine 5'-phosphosulfate to nitrogen of glucosamine in heparan sulfate. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BP6
?
Variant 5-150535762-C-T is Benign according to our data. Variant chr5-150535762-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 435948.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-4.59 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDST1 | NM_001543.5 | c.1314C>T | p.Pro438= | synonymous_variant | 6/15 | ENST00000261797.7 | |
NDST1 | NM_001301063.2 | c.1314C>T | p.Pro438= | synonymous_variant | 6/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDST1 | ENST00000261797.7 | c.1314C>T | p.Pro438= | synonymous_variant | 6/15 | 1 | NM_001543.5 | P1 | |
NDST1 | ENST00000523767.5 | c.1314C>T | p.Pro438= | synonymous_variant | 6/14 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 152226Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000641 AC: 16AN: 249560Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135076
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GnomAD4 exome AF: 0.000148 AC: 216AN: 1461858Hom.: 0 Cov.: 32 AF XY: 0.000132 AC XY: 96AN XY: 727234
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GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152344Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74492
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 25, 2015 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 02, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at