4-114997028-T-C

Position:

• chr4-114997028-T-C

Variant summary

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

The NM_022569.3(NDST4):​c.979-19754A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,866 control chromosomes in the GnomAD database, including 13,784 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 0.41 (13784 hom., cov: 32)
• Consequence: NDST4 NM_022569.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

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]

NDST4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NDST4	NM_022569.3	c.979-19754A>G		intron_variant		ENST00000264363.7	NP_072091.1
NDST4	XM_017008545.3	c.-159-19754A>G		intron_variant			XP_016864034.1
NDST4	XM_017008546.2	c.-71-26444A>G		intron_variant			XP_016864035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NDST4	ENST00000264363.7	c.979-19754A>G		intron_variant		1	NM_022569.3	ENSP00000264363.2
NDST4	ENST00000504854.1	n.-71-26444A>G		intron_variant		1		ENSP00000423218.1
NDST4	ENST00000613194.4	c.-159-19754A>G		intron_variant		5		ENSP00000483949.1
NDST4	ENST00000514570.1	n.407-19754A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62180 AN: 151746 Hom.: 13765 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.410 AC: 62253 AN: 151866 Hom.: 13784 Cov.: 32 AF XY: 0.414 AC XY: 30701 AN XY: 74238

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.448

Alfa AF: 0.349 Hom.: 2444

Bravo AF: 0.415

Asia WGS AF: 0.451 AC: 1571 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.36

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: rs2583513; hg19: chr4-115918184;