X-132877663-G-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001394073.1(HS6ST2):c.947+79145C>A 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 0.54 (12060 hom., 16737 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: HS6ST2 NM_001394073.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BS2: High Homozygotes in GnomAd at 12059 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HS6ST2	NM_001394073.1	c.947+79145C>A		intron_variant		ENST00000370833.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HS6ST2	ENST00000370833.7	c.947+79145C>A		intron_variant		5	NM_001394073.1

Frequencies

GnomAD3 genomes AF: 0.537 AC: 58931 AN: 109681 Hom.: 12059 Cov.: 22 AF XY: 0.522 AC XY: 16699 AN XY: 31965

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.575

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.517

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: 0.537 AC: 58962 AN: 109731 Hom.: 12060 Cov.: 22 AF XY: 0.523 AC XY: 16737 AN XY: 32025

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.515

Alfa AF: 0.541 Hom.: 4670

Bravo AF: 0.531

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.050
Dann	Benign	0.50

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: rs5933229; hg19: chrX-132011691;