Variant chr1-87084175-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_012262.4(HS2ST1):c.364-19A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.936 in 1,441,548 control chromosomes in the GnomAD database, including 632,089 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.92 ( 65015 hom., cov: 31)

Exomes 𝑓: 0.94 ( 567074 hom. )

Consequence

HS2ST1
NM_012262.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0340

Variant links:

Genes affected

HS2ST1 (HGNC:5193): (heparan sulfate 2-O-sulfotransferase 1) Heparan sulfate biosynthetic enzymes are key components in generating a myriad of distinct heparan sulfate fine structures that carry out multiple biologic activities. This gene encodes a member of the heparan sulfate biosynthetic enzyme family that transfers sulfate to the 2 position of the iduronic acid residue of heparan sulfate. The disruption of this gene resulted in no kidney formation in knockout embryonic mice, indicating that the absence of this enzyme may interfere with the signaling required for kidney formation. Two alternatively spliced transcript variants that encode different proteins have been found for this gene. [provided by RefSeq, Aug 2008]

HS2ST1 links:

ENSG00000267561 (HGNC:):

ENSG00000267561 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 1-87084175-A-G is Benign according to our data. Variant chr1-87084175-A-G is described in ClinVar as [Benign]. Clinvar id is 2585672.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HS2ST1	NM_012262.4 link	c.364-19A>G		intron_variant		ENST00000370550.10	NP_036394.1	Q7LGA3-1
HS2ST1	NM_001134492.2 link	c.364-19A>G		intron_variant			NP_001127964.1	Q7LGA3-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HS2ST1	ENST00000370550.10 link	c.364-19A>G		intron_variant		1	NM_012262.4	ENSP00000359581.4		Q7LGA3-1
ENSG00000267561	ENST00000370548.3 link	c.286-19A>G		intron_variant		2		ENSP00000359579.1

Frequencies

GnomAD3 genomes

AF:

0.924

AC:

140458

AN:

152090

Hom.:

64966

Cov.:

show subpopulations

Gnomad AFR

AF:

0.880

Gnomad AMI

AF:

0.948

Gnomad AMR

AF:

0.948

Gnomad ASJ

AF:

0.901

Gnomad EAS

AF:

0.994

Gnomad SAS

AF:

0.958

Gnomad FIN

AF:

0.948

Gnomad MID

AF:

0.902

Gnomad NFE

AF:

0.934

Gnomad OTH

AF:

0.929

GnomAD3 exomes

AF:

0.941

AC:

207790

AN:

220756

Hom.:

97915

AF XY:

0.941

AC XY:

112738

AN XY:

119746

show subpopulations

Gnomad AFR exome

AF:

0.875

Gnomad AMR exome

AF:

0.969

Gnomad ASJ exome

AF:

0.911

Gnomad EAS exome

AF:

0.996

Gnomad SAS exome

AF:

0.951

Gnomad FIN exome

AF:

0.950

Gnomad NFE exome

AF:

0.935

Gnomad OTH exome

AF:

0.936

GnomAD4 exome

AF:

0.938

AC:

1208892

AN:

1289340

Hom.:

567074

Cov.:

AF XY:

0.938

AC XY:

607355

AN XY:

647756

show subpopulations

Gnomad4 AFR exome

AF:

0.883

Gnomad4 AMR exome

AF:

0.966

Gnomad4 ASJ exome

AF:

0.908

Gnomad4 EAS exome

AF:

0.990

Gnomad4 SAS exome

AF:

0.950

Gnomad4 FIN exome

AF:

0.950

Gnomad4 NFE exome

AF:

0.936

Gnomad4 OTH exome

AF:

0.933

GnomAD4 genome

AF:

0.924

AC:

140565

AN:

152208

Hom.:

65015

Cov.:

AF XY:

0.927

AC XY:

68957

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.880

Gnomad4 AMR

AF:

0.948

Gnomad4 ASJ

AF:

0.901

Gnomad4 EAS

AF:

0.994

Gnomad4 SAS

AF:

0.958

Gnomad4 FIN

AF:

0.948

Gnomad4 NFE

AF:

0.934

Gnomad4 OTH

AF:

0.929

Alfa

AF:

0.919

Hom.:

13094

Bravo

AF:

0.924

Asia WGS

AF:

0.962

AC:

3339

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Neurofacioskeletal syndrome with or without renal agenesis

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.2

DANN

Benign

0.70

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