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GeneBe

rs5975352

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001394073.1(HS6ST2):c.948-55303T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 111,369 control chromosomes in the GnomAD database, including 1,004 homozygotes. There are 4,631 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 0.15 ( 1004 hom., 4631 hem., cov: 23)

Consequence

HS6ST2
NM_001394073.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.31
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HS6ST2NM_001394073.1 linkuse as main transcriptc.948-55303T>C intron_variant ENST00000370833.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HS6ST2ENST00000370833.7 linkuse as main transcriptc.948-55303T>C intron_variant 5 NM_001394073.1 Q96MM7-4

Frequencies

GnomAD3 genomes
AF:
0.148
AC:
16479
AN:
111319
Hom.:
1005
Cov.:
23
AF XY:
0.138
AC XY:
4631
AN XY:
33559
show subpopulations
Gnomad AFR
AF:
0.139
Gnomad AMI
AF:
0.0733
Gnomad AMR
AF:
0.0958
Gnomad ASJ
AF:
0.169
Gnomad EAS
AF:
0.288
Gnomad SAS
AF:
0.272
Gnomad FIN
AF:
0.105
Gnomad MID
AF:
0.170
Gnomad NFE
AF:
0.153
Gnomad OTH
AF:
0.154
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.148
AC:
16479
AN:
111369
Hom.:
1004
Cov.:
23
AF XY:
0.138
AC XY:
4631
AN XY:
33619
show subpopulations
Gnomad4 AFR
AF:
0.139
Gnomad4 AMR
AF:
0.0957
Gnomad4 ASJ
AF:
0.169
Gnomad4 EAS
AF:
0.287
Gnomad4 SAS
AF:
0.273
Gnomad4 FIN
AF:
0.105
Gnomad4 NFE
AF:
0.153
Gnomad4 OTH
AF:
0.154
Alfa
AF:
0.154
Hom.:
1653
Bravo
AF:
0.144

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
Cadd
Benign
6.4
Dann
Benign
0.64

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs5975352; hg19: chrX-131897825; API