X-132798388-T-G

Position:

• chrX-132798388-T-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001394073.1(HS6ST2):​c.948-89894A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.55 (12581 hom., 17006 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: HS6ST2 NM_001394073.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HS6ST2	NM_001394073.1	c.948-89894A>C		intron_variant		ENST00000370833.7	NP_001381002.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HS6ST2	ENST00000370833.7	c.948-89894A>C		intron_variant		5	NM_001394073.1	ENSP00000359870

Frequencies

GnomAD3 genomes AF: 0.547 AC: 60031 AN: 109672 Hom.: 12578 Cov.: 22 AF XY: 0.531 AC XY: 16964 AN XY: 31936

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.568

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.525

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.547 AC: 60069 AN: 109724 Hom.: 12581 Cov.: 22 AF XY: 0.531 AC XY: 17006 AN XY: 31998

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.524

Alfa AF: 0.444 Hom.: 4159

Bravo AF: 0.544

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.75

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: rs17317147; hg19: chrX-131932416;