1-21823667-G-T

Position:

chr1-21823667-G-T

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_005529.7(HSPG2):c.12952C>A(p.Arg4318=) variant causes a synonymous change. The variant allele was found at a frequency of 0.18 in 1,613,166 control chromosomes in the GnomAD database, including 28,135 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1837 hom., cov: 33)

Exomes 𝑓: 0.18 ( 26298 hom. )

Consequence

HSPG2
NM_005529.7 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 3.73

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:

LDLRAD2 (HGNC:32071): (low density lipoprotein receptor class A domain containing 2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LDLRAD2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.28).

BP6

Variant 1-21823667-G-T is Benign according to our data. Variant chr1-21823667-G-T is described in ClinVar as [Benign]. Clinvar id is 295701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-21823667-G-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSPG2	NM_005529.7 linkuse as main transcript	c.12952C>A	p.Arg4318=	synonymous_variant	96/97	ENST00000374695.8
LDLRAD2	NM_001013693.3 linkuse as main transcript	c.*1452G>T		3_prime_UTR_variant	5/5	ENST00000344642.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSPG2	ENST00000374695.8 linkuse as main transcript	c.12952C>A	p.Arg4318=	synonymous_variant	96/97	1	NM_005529.7	P1
LDLRAD2	ENST00000344642.7 linkuse as main transcript	c.*1452G>T		3_prime_UTR_variant	5/5	2	NM_001013693.3	P1

Frequencies

GnomAD3 genomes

AF:

0.140

AC:

21312

AN:

152066

Hom.:

1837

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0372

Gnomad AMI

AF:

0.0811

Gnomad AMR

AF:

0.128

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.167

Gnomad SAS

AF:

0.297

Gnomad FIN

AF:

0.241

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.176

Gnomad OTH

AF:

0.136

GnomAD3 exomes

AF:

0.178

AC:

44662

AN:

250734

Hom.:

4518

AF XY:

0.187

AC XY:

25400

AN XY:

135644

show subpopulations

Gnomad AFR exome

AF:

0.0345

Gnomad AMR exome

AF:

0.126

Gnomad ASJ exome

AF:

0.167

Gnomad EAS exome

AF:

0.160

Gnomad SAS exome

AF:

0.285

Gnomad FIN exome

AF:

0.235

Gnomad NFE exome

AF:

0.179

Gnomad OTH exome

AF:

0.169

GnomAD4 exome

AF:

0.184

AC:

269025

AN:

1460982

Hom.:

26298

Cov.:

AF XY:

0.187

AC XY:

136092

AN XY:

726844

show subpopulations

Gnomad4 AFR exome

AF:

0.0319

Gnomad4 AMR exome

AF:

0.127

Gnomad4 ASJ exome

AF:

0.174

Gnomad4 EAS exome

AF:

0.172

Gnomad4 SAS exome

AF:

0.282

Gnomad4 FIN exome

AF:

0.235

Gnomad4 NFE exome

AF:

0.182

Gnomad4 OTH exome

AF:

0.180

GnomAD4 genome

AF:

0.140

AC:

21310

AN:

152184

Hom.:

1837

Cov.:

AF XY:

0.144

AC XY:

10700

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.0371

Gnomad4 AMR

AF:

0.128

Gnomad4 ASJ

AF:

0.175

Gnomad4 EAS

AF:

0.167

Gnomad4 SAS

AF:

0.295

Gnomad4 FIN

AF:

0.241

Gnomad4 NFE

AF:

0.176

Gnomad4 OTH

AF:

0.138

Alfa

AF:

0.113

Hom.:

398

Bravo

AF:

0.126

Asia WGS

AF:

0.238

AC:

828

AN:

3478

EpiCase

AF:

0.164

EpiControl

AF:

0.177

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 19, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 11, 2023	- -

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 13, 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	Illumina Laboratory Services, Illumina	Jan 13, 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. -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Aug 10, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.28

CADD

Benign

DANN

Benign

0.94

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

2.7

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