rs2254358

Positions:

chr1-21890081-C-A

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The ENST00000374695.8(HSPG2):c.474G>T(p.Gly158=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 1,613,166 control chromosomes in the GnomAD database, including 328,190 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.53 ( 23646 hom., cov: 31)

Exomes 𝑓: 0.64 ( 304544 hom. )

Consequence

HSPG2
ENST00000374695.8 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: -0.592

Variant links:

Genes affected

HSPG2 (HGNC:5273): (heparan sulfate proteoglycan 2) This gene encodes the perlecan protein, which consists of a core protein to which three long chains of glycosaminoglycans (heparan sulfate or chondroitin sulfate) are attached. The perlecan protein is a large multidomain proteoglycan that binds to and cross-links many extracellular matrix components and cell-surface molecules. It has been shown that this protein interacts with laminin, prolargin, collagen type IV, FGFBP1, FBLN2, FGF7 and transthyretin, etc., and it plays essential roles in multiple biological activities. Perlecan is a key component of the vascular extracellular matrix, where it helps to maintain the endothelial barrier function. It is a potent inhibitor of smooth muscle cell proliferation and is thus thought to help maintain vascular homeostasis. It can also promote growth factor (e.g., FGF2) activity and thus stimulate endothelial growth and re-generation. It is a major component of basement membranes, where it is involved in the stabilization of other molecules as well as being involved with glomerular permeability to macromolecules and cell adhesion. Mutations in this gene cause Schwartz-Jampel syndrome type 1, Silverman-Handmaker type of dyssegmental dysplasia, and tardive dyskinesia. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014]

HSPG2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.34).

BP6

Variant 1-21890081-C-A is Benign according to our data. Variant chr1-21890081-C-A is described in ClinVar as [Benign]. Clinvar id is 295910.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-21890081-C-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.592 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HSPG2	NM_005529.7 linkuse as main transcript	c.474G>T	p.Gly158=	synonymous_variant	6/97	ENST00000374695.8	NP_005520.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
HSPG2	ENST00000374695.8 linkuse as main transcript	c.474G>T	p.Gly158=	synonymous_variant	6/97	1	NM_005529.7	ENSP00000363827	P1
HSPG2	ENST00000374673.4 linkuse as main transcript	c.231G>T	p.Gly77=	synonymous_variant	3/7	3		ENSP00000497688
HSPG2	ENST00000412328.5 linkuse as main transcript	n.242G>T		non_coding_transcript_exon_variant	3/6	2
HSPG2	ENST00000439717.2 linkuse as main transcript	n.372G>T		non_coding_transcript_exon_variant	5/5	2

Frequencies

GnomAD3 genomes

AF:

0.532

AC:

80751

AN:

151752

Hom.:

23644

Cov.:

show subpopulations

Gnomad AFR

AF:

0.295

Gnomad AMI

AF:

0.515

Gnomad AMR

AF:

0.484

Gnomad ASJ

AF:

0.758

Gnomad EAS

AF:

0.369

Gnomad SAS

AF:

0.601

Gnomad FIN

AF:

0.644

Gnomad MID

AF:

0.712

Gnomad NFE

AF:

0.664

Gnomad OTH

AF:

0.570

GnomAD3 exomes

AF:

0.577

AC:

145150

AN:

251382

Hom.:

44245

AF XY:

0.594

AC XY:

80668

AN XY:

135876

show subpopulations

Gnomad AFR exome

AF:

0.290

Gnomad AMR exome

AF:

0.416

Gnomad ASJ exome

AF:

0.747

Gnomad EAS exome

AF:

0.374

Gnomad SAS exome

AF:

0.597

Gnomad FIN exome

AF:

0.642

Gnomad NFE exome

AF:

0.666

Gnomad OTH exome

AF:

0.603

GnomAD4 exome

AF:

0.640

AC:

934702

AN:

1461298

Hom.:

304544

Cov.:

AF XY:

0.641

AC XY:

466034

AN XY:

727006

show subpopulations

Gnomad4 AFR exome

AF:

0.286

Gnomad4 AMR exome

AF:

0.425

Gnomad4 ASJ exome

AF:

0.750

Gnomad4 EAS exome

AF:

0.406

Gnomad4 SAS exome

AF:

0.594

Gnomad4 FIN exome

AF:

0.635

Gnomad4 NFE exome

AF:

0.669

Gnomad4 OTH exome

AF:

0.621

GnomAD4 genome

AF:

0.532

AC:

80763

AN:

151868

Hom.:

23646

Cov.:

AF XY:

0.530

AC XY:

39320

AN XY:

74198

show subpopulations

Gnomad4 AFR

AF:

0.294

Gnomad4 AMR

AF:

0.483

Gnomad4 ASJ

AF:

0.758

Gnomad4 EAS

AF:

0.369

Gnomad4 SAS

AF:

0.601

Gnomad4 FIN

AF:

0.644

Gnomad4 NFE

AF:

0.664

Gnomad4 OTH

AF:

0.572

Alfa

AF:

0.645

Hom.:

61575

Bravo

AF:

0.512

Asia WGS

AF:

0.496

AC:

1724

AN:

3478

EpiCase

AF:

0.675

EpiControl

AF:

0.689

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 23, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Feb 08, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Lethal Kniest-like syndrome

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Aug 10, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 12, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Schwartz-Jampel syndrome

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Aug 10, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 12, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

1.7

DANN

Uncertain

0.98

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