5-150521397-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001543.5(NDST1):c.143C>T(p.Ser48Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000174 in 1,613,140 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000018 ( 0 hom. )
Consequence
NDST1
NM_001543.5 missense
NM_001543.5 missense
Scores
3
4
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.99
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.14202553).
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NDST1 | ENST00000261797.7 | c.143C>T | p.Ser48Leu | missense_variant | Exon 2 of 15 | 1 | NM_001543.5 | ENSP00000261797.6 | ||
NDST1 | ENST00000523767.5 | c.143C>T | p.Ser48Leu | missense_variant | Exon 2 of 14 | 2 | ENSP00000428604.1 | |||
NDST1 | ENST00000519157.1 | c.143C>T | p.Ser48Leu | missense_variant | Exon 2 of 2 | 5 | ENSP00000427813.1 | |||
NDST1 | ENST00000522491.1 | c.143C>T | p.Ser48Leu | missense_variant | Exon 2 of 2 | 2 | ENSP00000429966.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000281 AC: 7AN: 248676Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134660
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GnomAD4 exome AF: 0.0000178 AC: 26AN: 1460976Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 726862
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74330
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;.;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;.;.;L
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;N;N;N
REVEL
Benign
Sift
Pathogenic
D;T;T;T
Sift4G
Pathogenic
D;T;T;T
Polyphen
0.0040, 0.021
.;.;B;B
Vest4
0.20, 0.18
MutPred
Loss of glycosylation at S48 (P = 0.0122);Loss of glycosylation at S48 (P = 0.0122);Loss of glycosylation at S48 (P = 0.0122);Loss of glycosylation at S48 (P = 0.0122);
MVP
MPC
0.60
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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