Variant 2-128268131-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004807.3(HS6ST1):c.*31G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.077 in 1,516,644 control chromosomes in the GnomAD database, including 4,776 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.071 ( 402 hom., cov: 33)

Exomes 𝑓: 0.078 ( 4374 hom. )

Consequence

HS6ST1
NM_004807.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.50

Variant links:

Genes affected

HS6ST1 (HGNC:5201): (heparan sulfate 6-O-sulfotransferase 1) The protein encoded by this gene is a member of the heparan sulfate biosynthetic enzyme family. Heparan sulfate biosynthetic enzymes are key components in generating a myriad of distinct heparan sulfate fine structures that carry out multiple biological activities. This enzyme is a type II integral membrane protein and is responsible for 6-O-sulfation of heparan sulfate. This enzyme does not share significant sequence similarity with other known sulfotransferases. A pseudogene located on chromosome 1 has been found for this gene. [provided by RefSeq, Jul 2008]

HS6ST1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 2-128268131-C-G is Benign according to our data. Variant chr2-128268131-C-G is described in ClinVar as [Benign]. Clinvar id is 1226324.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HS6ST1	NM_004807.3 link	c.*31G>C		3_prime_UTR_variant	Exon 2 of 2	ENST00000259241.7	NP_004798.3	O60243-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HS6ST1	ENST00000259241 link	c.*31G>C		3_prime_UTR_variant	Exon 2 of 2	1	NM_004807.3	ENSP00000259241.6		O60243-1
HS6ST1	ENST00000469019.1 link	n.361-21606G>C		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes

AF:

0.0715

AC:

10870

AN:

152048

Hom.:

402

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0730

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0735

Gnomad ASJ

AF:

0.0541

Gnomad EAS

AF:

0.0245

Gnomad SAS

AF:

0.0222

Gnomad FIN

AF:

0.0416

Gnomad MID

AF:

0.134

Gnomad NFE

AF:

0.0824

Gnomad OTH

AF:

0.0989

GnomAD3 exomes

AF:

0.0605

AC:

11094

AN:

183486

Hom.:

366

AF XY:

0.0603

AC XY:

6048

AN XY:

100368

show subpopulations

Gnomad AFR exome

AF:

0.0674

Gnomad AMR exome

AF:

0.0525

Gnomad ASJ exome

AF:

0.0499

Gnomad EAS exome

AF:

0.0262

Gnomad SAS exome

AF:

0.0289

Gnomad FIN exome

AF:

0.0415

Gnomad NFE exome

AF:

0.0837

Gnomad OTH exome

AF:

0.0745

GnomAD4 exome

AF:

0.0776

AC:

105903

AN:

1364478

Hom.:

4374

Cov.:

AF XY:

0.0759

AC XY:

51537

AN XY:

679008

show subpopulations

Gnomad4 AFR exome

AF:

0.0720

Gnomad4 AMR exome

AF:

0.0571

Gnomad4 ASJ exome

AF:

0.0514

Gnomad4 EAS exome

AF:

0.0265

Gnomad4 SAS exome

AF:

0.0284

Gnomad4 FIN exome

AF:

0.0454

Gnomad4 NFE exome

AF:

0.0860

Gnomad4 OTH exome

AF:

0.0813

GnomAD4 genome

AF:

0.0715

AC:

10875

AN:

152166

Hom.:

402

Cov.:

AF XY:

0.0687

AC XY:

5110

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.0730

Gnomad4 AMR

AF:

0.0734

Gnomad4 ASJ

AF:

0.0541

Gnomad4 EAS

AF:

0.0249

Gnomad4 SAS

AF:

0.0224

Gnomad4 FIN

AF:

0.0416

Gnomad4 NFE

AF:

0.0824

Gnomad4 OTH

AF:

0.0974

Alfa

AF:

0.0366

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Aug 30, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.4

DANN

Benign

0.73

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over