rs6824418

chr4-118187620-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004784.3(NDST3):c.1540-36871G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0616 in 152,076 control chromosomes in the GnomAD database, including 607 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 0.062 (607 hom., cov: 32)
• Consequence: NDST3 NM_004784.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

Genes affected

NDST3 (HGNC:7682): (N-deacetylase and N-sulfotransferase 3) 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. This monomeric bifunctional enzyme catalyzes the N-deacetylation and N-sulfation of N-acetylglucosamine residues in heparan sulfate and heparin, which are the initial chemical modifications required for the biosynthesis of the functional oligosaccharide sequences that define the specific ligand binding activities of heparan sulfate and heparin. [provided by RefSeq, Nov 2008]

LOC107986307 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NDST3	NM_004784.3	c.1540-36871G>T		intron_variant		ENST00000296499.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NDST3	ENST00000296499.6	c.1540-36871G>T		intron_variant		1	NM_004784.3	P1

Frequencies

GnomAD3 genomes AF: 0.0614 AC: 9334 AN: 151958 Hom.: 601 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0527

Gnomad AMR AF: 0.0273

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.00367

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0245

Gnomad OTH AF: 0.0494

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0616 AC: 9363 AN: 152076 Hom.: 607 Cov.: 32 AF XY: 0.0587 AC XY: 4367 AN XY: 74336

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0273

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.00368

Gnomad4 SAS AF: 0.0340

Gnomad4 FIN AF: 0.0103

Gnomad4 NFE AF: 0.0245

Gnomad4 OTH AF: 0.0489

Alfa AF: 0.0401 Hom.: 92

Bravo AF: 0.0671

Asia WGS AF: 0.0380 AC: 134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.25
Dann	Benign	0.16

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6824418; hg19: chr4-119108775;