rs2583513

Variant names:

• chr4-114997028-T-A
• rs2583513
• NM_022569.3:c.979-19754A>T

Your query was ambiguous. Multiple possible variants found:

• chr4-114997028-T-A
• chr4-114997028-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_022569.3(NDST4):​c.979-19754A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: NDST4 NM_022569.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDST4	NM_022569.3	c.979-19754A>T		intron_variant	Intron 2 of 13	ENST00000264363.7	NP_072091.1
NDST4	XM_017008545.3	c.-159-19754A>T		intron_variant	Intron 1 of 12		XP_016864034.1
NDST4	XM_017008546.2	c.-71-26444A>T		intron_variant	Intron 1 of 11		XP_016864035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NDST4	ENST00000264363.7	c.979-19754A>T		intron_variant	Intron 2 of 13	1	NM_022569.3	ENSP00000264363.2
NDST4	ENST00000504854.1	n.-71-26444A>T		intron_variant	Intron 1 of 12	1		ENSP00000423218.1
NDST4	ENST00000613194.4	c.-159-19754A>T		intron_variant	Intron 2 of 14	5		ENSP00000483949.1
NDST4	ENST00000514570.1	n.407-19754A>T		intron_variant	Intron 1 of 5	2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.40
PhyloP100		0.23

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

Other links and lift over

dbSNP: rs2583513; hg19: chr4-115918184;