10-73808190-G-C

Variant names:

• chr10-73808190-G-C
• rs141599100
• NM_003635.4:c.199C>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_003635.4(NDST2):​c.199C>G​(p.Arg67Gly) variant causes a missense 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. 15/21 in silico tools predict 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: NDST2 NM_003635.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42

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]

ENSG00000272916 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.12010768).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDST2	NM_003635.4	c.199C>G	p.Arg67Gly	missense_variant	Exon 3 of 15	ENST00000309979.11	NP_003626.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NDST2	ENST00000309979.11	c.199C>G	p.Arg67Gly	missense_variant	Exon 3 of 15	1	NM_003635.4	ENSP00000310657.6
NDST2	ENST00000299641.8	c.199C>G	p.Arg67Gly	missense_variant	Exon 1 of 13	1		ENSP00000299641.5
ENSG00000272916	ENST00000603027.5	n.199C>G		non_coding_transcript_exon_variant	Exon 3 of 17	2		ENSP00000475031.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ExAC AF: 0.00000824 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.075
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Benign	13
DANN	Benign	0.96
DEOGEN2	Benign	0.24	T;T;.
Eigen	Benign	-0.59
Eigen_PC	Benign	-0.60
FATHMM_MKL	Benign	0.25	N
LIST_S2	Benign	0.74	T;.;.
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.12	T;T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	0.0	N;N;.
PrimateAI	Benign	0.46	T
PROVEAN	Benign	-1.1	.;N;.
REVEL	Benign	0.14
Sift	Benign	0.24	.;T;.
Sift4G	Benign	0.48	T;T;.
Polyphen		0.048	B;B;.
Vest4		0.28
MutPred		0.29		Loss of methylation at R67 (P = 0.0106);Loss of methylation at R67 (P = 0.0106);Loss of methylation at R67 (P = 0.0106);
MVP		0.39
MPC		0.78
ClinPred		0.10	T
GERP RS		-0.064
Varity_R		0.11
gMVP		0.37

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: rs141599100; hg19: chr10-75567948;