chrX-132863823-C-T

Position:

• chrX-132863823-C-T

Variant summary

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

The NM_001394073.1(HS6ST2):​c.947+92985G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 111,093 control chromosomes in the GnomAD database, including 909 homozygotes. There are 4,399 hemizygotes in GnomAD. 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 0.14 (909 hom., 4399 hem., cov: 22)
• Consequence: HS6ST2 NM_001394073.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

Genes affected

HS6ST2 (HGNC:19133): (heparan sulfate 6-O-sulfotransferase 2) Heparan sulfate proteoglycans are ubiquitous components of the cell surface, extracellular matrix, and basement membranes, and interact with various ligands to influence cell growth, differentiation, adhesion, and migration. This gene encodes a member of the heparan sulfate (HS) sulfotransferase gene family, which catalyze the transfer of sulfate to HS. Different family members and isoforms are thought to synthesize heparan sulfates with tissue-specific structures and functions. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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 (EAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HS6ST2	NM_001394073.1	c.947+92985G>A		intron_variant		ENST00000370833.7	NP_001381002.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HS6ST2	ENST00000370833.7	c.947+92985G>A		intron_variant		5	NM_001394073.1	ENSP00000359870.3

Frequencies

GnomAD3 genomes AF: 0.138 AC: 15290 AN: 111042 Hom.: 911 Cov.: 22 AF XY: 0.132 AC XY: 4400 AN XY: 33296

Gnomad AFR AF: 0.0811

Gnomad AMI AF: 0.0751

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.246

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.138 AC: 15282 AN: 111093 Hom.: 909 Cov.: 22 AF XY: 0.132 AC XY: 4399 AN XY: 33357

Gnomad4 AFR AF: 0.0810

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.147

Alfa AF: 0.159 Hom.: 9871

Bravo AF: 0.133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.72

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: rs17324216; hg19: chrX-131997851;