rs4691

Variant names:

• chr10-73802158-T-A
• rs4691
• NM_003635.4:c.*293A>T

Your query was ambiguous. Multiple possible variants found:

• chr10-73802158-T-A
• chr10-73802158-T-C

Variant summary

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

The NM_003635.4(NDST2):​c.*293A>T variant causes a 3 prime UTR 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: 33)
• Consequence: NDST2 NM_003635.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.78
• Publications: 31 publications found

Genes affected

NDST2 (HGNC:7681): (N-deacetylase and N-sulfotransferase 2) This gene encodes a member of the N-deacetylase/N-sulfotransferase subfamily of the sulfotransferase 1 proteins. The encoded enzyme has dual functions in processing glucosamine and heparin polymers, including N-deacetylation and N-sulfation. The encoded protein may be localized to the Golgi. [provided by RefSeq, Feb 2009]

NDST2 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ENSG00000272916 (HGNC:):

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=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003635.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NDST2	NM_003635.4	MANE Select	c.*293A>T		3_prime_UTR	Exon 15 of 15	NP_003626.1	P52849-1
	NDST2	NM_001330107.2		c.*460A>T		3_prime_UTR	Exon 15 of 15	NP_001317036.1	S4R438
	NDST2	NR_160743.1		n.3767A>T		non_coding_transcript_exon	Exon 15 of 15

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NDST2	ENST00000309979.11	TSL:1 MANE Select	c.*293A>T		3_prime_UTR	Exon 15 of 15	ENSP00000310657.6	P52849-1
	NDST2	ENST00000299641.8	TSL:1	c.*293A>T		3_prime_UTR	Exon 13 of 13	ENSP00000299641.5	P52849-1
	ENSG00000272916	ENST00000603027.5	TSL:2	n.*557A>T		non_coding_transcript_exon	Exon 14 of 17	ENSP00000475031.1	S4R438

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 3

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.0090
DANN	Benign	0.69
PhyloP100		-5.8

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: rs4691; hg19: chr10-75561916;