chr4-114908763-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022569.3(NDST4):c.1536+26443C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,044 control chromosomes in the GnomAD database, including 8,152 homozygotes. 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 0.29 ( 8152 hom., cov: 32)
Consequence
NDST4
NM_022569.3 intron
NM_022569.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.176
Genes affected
NDST4 (HGNC:20779): (N-deacetylase and N-sulfotransferase 4) Predicted to enable [heparan sulfate]-glucosamine N-sulfotransferase activity and deacetylase activity. Predicted to be involved in heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process. Predicted to be located in Golgi membrane. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDST4 | NM_022569.3 | c.1536+26443C>T | intron_variant | ENST00000264363.7 | |||
NDST4 | XM_017008545.3 | c.399+26443C>T | intron_variant | ||||
NDST4 | XM_017008546.2 | c.399+26443C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDST4 | ENST00000264363.7 | c.1536+26443C>T | intron_variant | 1 | NM_022569.3 | P1 | |||
NDST4 | ENST00000504854.1 | c.399+26443C>T | intron_variant, NMD_transcript_variant | 1 | |||||
NDST4 | ENST00000613194.4 | c.399+26443C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.287 AC: 43589AN: 151926Hom.: 8128 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.287 AC: 43666AN: 152044Hom.: 8152 Cov.: 32 AF XY: 0.296 AC XY: 21967AN XY: 74310
GnomAD4 genome
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1122
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3460
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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