Variant rs34029730 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_000199.5(SGSH):c.664-39_664-38delCT variant causes a intron 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
NM_000199.5 intron

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 0.504

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:

SGSH (HGNC:):

SGSH links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SGSH	NM_000199.5 linkuse as main transcript	c.664-39_664-38delCT		intron_variant		ENST00000326317.11	NP_000190.1	P51688

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SGSH	ENST00000326317.11 linkuse as main transcript	c.664-39_664-38delCT		intron_variant		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

GnomAD3 exomes

AF:

0.382

AC:

80474

AN:

210600

Hom.:

15931

AF XY:

0.378

AC XY:

43494

AN XY:

115040

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 SAS exome

AF:

0.411

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

Gnomad4 AFR exome

AF:

0.185

Gnomad4 AMR exome

AF:

0.535

Gnomad4 ASJ exome

AF:

0.359

Gnomad4 EAS exome

AF:

0.340

Gnomad4 SAS exome

AF:

0.404

Gnomad4 FIN exome

AF:

0.369

Gnomad4 NFE exome

AF:

0.345

Gnomad4 OTH exome

AF:

0.355

GnomAD4 genome

AF:

0.319

AC:

48350

AN:

151728

Hom.:

8175

Cov.:

AF XY:

0.322

AC XY:

23870

AN XY:

74124

show subpopulations

Gnomad4 AFR

AF:

0.195

Gnomad4 AMR

AF:

0.460

Gnomad4 ASJ

AF:

0.358

Gnomad4 EAS

AF:

0.400

Gnomad4 SAS

AF:

0.410

Gnomad4 FIN

AF:

0.355

Gnomad4 NFE

AF:

0.343

Gnomad4 OTH

AF:

0.353

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

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Nov 07, 2021	- -
Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 27, 2019	- -

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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