rs7881124

chrX-132760716-A-GchrX-132760716-A-T

Variant summary

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

The NM_001394073.1(HS6ST2):c.948-52222T>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 0.58 (13928 hom., 17655 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: HS6ST2 NM_001394073.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.794

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=-1.0).
• BS2: High Homozygotes in GnomAd at 13926 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HS6ST2	NM_001394073.1	c.948-52222T>C		intron_variant		ENST00000370833.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HS6ST2	ENST00000370833.7	c.948-52222T>C		intron_variant		5	NM_001394073.1

Frequencies

GnomAD3 genomes AF: 0.575 AC: 62892 AN: 109414 Hom.: 13926 Cov.: 22 AF XY: 0.555 AC XY: 17594 AN XY: 31694

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.651

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.558

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: 0.575 AC: 62946 AN: 109469 Hom.: 13928 Cov.: 22 AF XY: 0.556 AC XY: 17655 AN XY: 31759

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.556

Alfa AF: 0.524 Hom.: 25197

Bravo AF: 0.572

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.29
Dann	Benign	0.36

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: rs7881124; hg19: chrX-131894744;