rs148765445
Positions:
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_001543.5(NDST1):c.2589G>A(p.Leu863=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000345 in 1,613,948 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0017 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00020 ( 1 hom. )
Consequence
NDST1
NM_001543.5 synonymous
NM_001543.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.37
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]
Genome browser will be placed here
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=-0.38).
BP6
?
Variant 5-150553272-G-A is Benign according to our data. Variant chr5-150553272-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 435957.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=2.37 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDST1 | NM_001543.5 | c.2589G>A | p.Leu863= | synonymous_variant | 15/15 | ENST00000261797.7 | |
NDST1 | NM_001301063.2 | c.2418G>A | p.Leu806= | synonymous_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDST1 | ENST00000261797.7 | c.2589G>A | p.Leu863= | synonymous_variant | 15/15 | 1 | NM_001543.5 | P1 | |
NDST1 | ENST00000523767.5 | c.2418G>A | p.Leu806= | synonymous_variant | 14/14 | 2 | |||
NDST1 | ENST00000521752.1 | n.130G>A | non_coding_transcript_exon_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00173 AC: 264AN: 152206Hom.: 0 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
264
AN:
152206
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000521 AC: 131AN: 251474Hom.: 0 AF XY: 0.000434 AC XY: 59AN XY: 135912
GnomAD3 exomes
AF:
AC:
131
AN:
251474
Hom.:
AF XY:
AC XY:
59
AN XY:
135912
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000200 AC: 292AN: 1461624Hom.: 1 Cov.: 31 AF XY: 0.000179 AC XY: 130AN XY: 727114
GnomAD4 exome
AF:
AC:
292
AN:
1461624
Hom.:
Cov.:
31
AF XY:
AC XY:
130
AN XY:
727114
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00174 AC: 265AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.00164 AC XY: 122AN XY: 74496
GnomAD4 genome
?
AF:
AC:
265
AN:
152324
Hom.:
Cov.:
32
AF XY:
AC XY:
122
AN XY:
74496
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign/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 | Oct 20, 2015 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 14, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at