chr10-73802158-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003635.4(NDST2):​c.*293A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 497,384 control chromosomes in the GnomAD database, including 19,907 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 0.23 (4920 hom., cov: 33)
  • Exomes 𝑓: 0.28 (14987 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

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>G		3_prime_UTR	Exon 15 of 15	NP_003626.1	P52849-1
	NDST2	NM_001330107.2		c.*460A>G		3_prime_UTR	Exon 15 of 15	NP_001317036.1	S4R438
	NDST2	NR_160743.1		n.3767A>G		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>G		3_prime_UTR	Exon 15 of 15	ENSP00000310657.6	P52849-1
	NDST2	ENST00000299641.8	TSL:1	c.*293A>G		3_prime_UTR	Exon 13 of 13	ENSP00000299641.5	P52849-1
	ENSG00000272916	ENST00000603027.5	TSL:2	n.*557A>G		non_coding_transcript_exon	Exon 14 of 17	ENSP00000475031.1	S4R438

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35653 AN: 152068 Hom.: 4916 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.176

GnomAD4 exome AF: 0.275 AC: 95018 AN: 345198 Hom.: 14987 Cov.: 3 AF XY: 0.279 AC XY: 50626 AN XY: 181414

African (AFR) AF: 0.117 AC: 1240 AN: 10590

American (AMR) AF: 0.278 AC: 3322 AN: 11938

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 1148 AN: 11074

East Asian (EAS) AF: 0.481 AC: 10960 AN: 22784

South Asian (SAS) AF: 0.362 AC: 13228 AN: 36564

European-Finnish (FIN) AF: 0.370 AC: 7822 AN: 21152

Middle Eastern (MID) AF: 0.0916 AC: 147 AN: 1604

European-Non Finnish (NFE) AF: 0.249 AC: 52157 AN: 209244

Other (OTH) AF: 0.247 AC: 4994 AN: 20248

GnomAD4 genome AF: 0.234 AC: 35662 AN: 152186 Hom.: 4920 Cov.: 33 AF XY: 0.243 AC XY: 18070 AN XY: 74408

African (AFR) AF: 0.120 AC: 4998 AN: 41542

American (AMR) AF: 0.246 AC: 3768 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0916 AC: 318 AN: 3472

East Asian (EAS) AF: 0.514 AC: 2658 AN: 5172

South Asian (SAS) AF: 0.388 AC: 1872 AN: 4828

European-Finnish (FIN) AF: 0.375 AC: 3967 AN: 10582

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17393 AN: 67982

Other (OTH) AF: 0.180 AC: 379 AN: 2110

Alfa AF: 0.235 Hom.: 7755

Bravo AF: 0.219

Asia WGS AF: 0.446 AC: 1548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.015
DANN	Benign	0.61
PhyloP100		-5.8
Mutation Taster		=100/0	polymorphism (auto)

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;