rs34029730

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The ENST00000575282.5(SGSH):n.920_921delCT variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 1,577,990 control chromosomes in the GnomAD database, including 98,466 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 8175 hom., cov: 0)

Exomes 𝑓: 0.35 ( 90291 hom. )

Consequence

SGSH
ENST00000575282.5 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.504

Publications

5 publications found

Variant links:

Genes affected

SGSH (HGNC:10818): (N-sulfoglucosamine sulfohydrolase) This gene encodes the enzyme sulfamidase; one of several enzymes involved in the lysosomal degradation of heparan sulfate. Mutations in this gene are associated with the lysosomal storage disease mucopolysaccaridosis IIIA, also known as Sanfilippo syndrome A, which results from impaired degradation of heparan sulfate. Transcripts of varying sizes have been reported but their biological validity has not been determined. [provided by RefSeq, Jun 2017]

SGSH links:

CARD14 (HGNC:16446): (caspase recruitment domain family member 14) This gene encodes a caspase recruitment domain-containing protein that is a member of the membrane-associated guanylate kinase (MAGUK) family of proteins. Members of this protein family are scaffold proteins that are involved in a diverse array of cellular processes including cellular adhesion, signal transduction and cell polarity control. This protein has been shown to specifically interact with BCL10, a protein known to function as a positive regulator of cell apoptosis and NF-kappaB activation. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2012]

CARD14 Gene-Disease associations (from GenCC):

familial pityriasis rubra pilaris
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet, Genomics England PanelApp
psoriasis 2
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Genomics England PanelApp

CARD14 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP6

Variant 17-80213922-CAG-C is Benign according to our data. Variant chr17-80213922-CAG-C is described in ClinVar as [Likely_benign]. Clinvar id is 255518.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SGSH	NM_000199.5 link	c.664-39_664-38delCT		intron_variant	Intron 5 of 7	ENST00000326317.11	NP_000190.1	P51688

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGSH	ENST00000326317.11 link	c.664-39_664-38delCT		intron_variant	Intron 5 of 7	1	NM_000199.5	ENSP00000314606.6		P51688

Frequencies

GnomAD3 genomes

AF:

0.319

AC:

48304

AN:

151612

Hom.:

8158

Cov.:

show subpopulations

Gnomad AFR

AF:

0.195

Gnomad AMI

AF:

0.199

Gnomad AMR

AF:

0.459

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.400

Gnomad SAS

AF:

0.410

Gnomad FIN

AF:

0.355

Gnomad MID

AF:

0.331

Gnomad NFE

AF:

0.343

Gnomad OTH

AF:

0.352

GnomAD2 exomes

AF:

0.382

AC:

80474

AN:

210600

AF XY:

0.378

show subpopulations

Gnomad AFR exome

AF:

0.193

Gnomad AMR exome

AF:

0.546

Gnomad ASJ exome

AF:

0.361

Gnomad EAS exome

AF:

0.425

Gnomad FIN exome

AF:

0.381

Gnomad NFE exome

AF:

0.344

Gnomad OTH exome

AF:

0.373

GnomAD4 exome

AF:

0.352

AC:

501882

AN:

1426262

Hom.:

90291

AF XY:

0.354

AC XY:

250982

AN XY:

709416

show subpopulations

African (AFR)

AF:

0.185

AC:

6136

AN:

33180

American (AMR)

AF:

0.535

AC:

22075

AN:

41266

Ashkenazi Jewish (ASJ)

AF:

0.359

AC:

9192

AN:

25588

East Asian (EAS)

AF:

0.340

AC:

13279

AN:

39008

South Asian (SAS)

AF:

0.404

AC:

33729

AN:

83404

European-Finnish (FIN)

AF:

0.369

AC:

16094

AN:

43566

Middle Eastern (MID)

AF:

0.354

AC:

2018

AN:

5706

European-Non Finnish (NFE)

AF:

0.345

AC:

378285

AN:

1095140

Other (OTH)

AF:

0.355

AC:

21074

AN:

59404

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

17391

34781

52172

69562

86953

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.319

AC:

48350

AN:

151728

Hom.:

8175

Cov.:

AF XY:

0.322

AC XY:

23870

AN XY:

74124

show subpopulations

African (AFR)

AF:

0.195

AC:

8087

AN:

41470

American (AMR)

AF:

0.460

AC:

7001

AN:

15230

Ashkenazi Jewish (ASJ)

AF:

0.358

AC:

1239

AN:

3458

East Asian (EAS)

AF:

0.400

AC:

2046

AN:

5120

South Asian (SAS)

AF:

0.410

AC:

1973

AN:

4808

European-Finnish (FIN)

AF:

0.355

AC:

3741

AN:

10530

Middle Eastern (MID)

AF:

0.345

AC:

100

AN:

290

European-Non Finnish (NFE)

AF:

0.343

AC:

23240

AN:

67814

Other (OTH)

AF:

0.353

AC:

742

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1651

3302

4954

6605

8256

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.337

Hom.:

1599

Bravo

AF:

0.324

Asia WGS

AF:

0.394

AC:

1369

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Mucopolysaccharidosis, MPS-III-A

Benign:2

Nov 07, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Sep 27, 2019

Natera, Inc.

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Mar 03, 2015

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.50

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs34029730

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over