rs1800428

Positions:

chr15-72375964-G-A

Variant summary

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

The NM_000520.6(HEXA):c.9C>T(p.Ser3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0424 in 1,613,708 control chromosomes in the GnomAD database, including 1,833 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.033 ( 131 hom., cov: 32)

Exomes 𝑓: 0.043 ( 1702 hom. )

Consequence

HEXA
NM_000520.6 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:13

Conservation

PhyloP100: 0.521

Variant links:

Genes affected

HEXA (HGNC:4878): (hexosaminidase subunit alpha) This gene encodes a member of the glycosyl hydrolase 20 family of proteins. The encoded preproprotein is proteolytically processed to generate the alpha subunit of the lysosomal enzyme beta-hexosaminidase. This enzyme, together with the cofactor GM2 activator protein, catalyzes the degradation of the ganglioside GM2, and other molecules containing terminal N-acetyl hexosamines. Mutations in this gene lead to an accumulation of GM2 ganglioside in neurons, the underlying cause of neurodegenerative disorders termed the GM2 gangliosidoses, including Tay-Sachs disease (GM2-gangliosidosis type I). Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. [provided by RefSeq, Jan 2016]

HEXA 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=-0.45).

BP6

Variant 15-72375964-G-A is Benign according to our data. Variant chr15-72375964-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 93193.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-72375964-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.521 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
HEXA	NM_000520.6 linkuse as main transcript	c.9C>T	p.Ser3=	synonymous_variant	1/14	ENST00000268097.10
HEXA	NM_001318825.2 linkuse as main transcript	c.9C>T	p.Ser3=	synonymous_variant	1/14
HEXA	NR_134869.3 linkuse as main transcript	n.51C>T		non_coding_transcript_exon_variant	1/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HEXA	ENST00000268097.10 linkuse as main transcript	c.9C>T	p.Ser3=	synonymous_variant	1/14	1	NM_000520.6	P1	P06865-1

Frequencies

GnomAD3 genomes

AF:

0.0329

AC:

5011

AN:

152202

Hom.:

132

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00789

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.0252

Gnomad ASJ

AF:

0.0179

Gnomad EAS

AF:

0.114

Gnomad SAS

AF:

0.0510

Gnomad FIN

AF:

0.0210

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0441

Gnomad OTH

AF:

0.0320

GnomAD3 exomes

AF:

0.0415

AC:

10372

AN:

250098

Hom.:

289

AF XY:

0.0427

AC XY:

5777

AN XY:

135386

show subpopulations

Gnomad AFR exome

AF:

0.00791

Gnomad AMR exome

AF:

0.0269

Gnomad ASJ exome

AF:

0.0190

Gnomad EAS exome

AF:

0.113

Gnomad SAS exome

AF:

0.0472

Gnomad FIN exome

AF:

0.0231

Gnomad NFE exome

AF:

0.0431

Gnomad OTH exome

AF:

0.0395

GnomAD4 exome

AF:

0.0433

AC:

63351

AN:

1461388

Hom.:

1702

Cov.:

AF XY:

0.0438

AC XY:

31878

AN XY:

727000

show subpopulations

Gnomad4 AFR exome

AF:

0.00618

Gnomad4 AMR exome

AF:

0.0263

Gnomad4 ASJ exome

AF:

0.0172

Gnomad4 EAS exome

AF:

0.139

Gnomad4 SAS exome

AF:

0.0467

Gnomad4 FIN exome

AF:

0.0241

Gnomad4 NFE exome

AF:

0.0432

Gnomad4 OTH exome

AF:

0.0395

GnomAD4 genome

AF:

0.0329

AC:

5007

AN:

152320

Hom.:

131

Cov.:

AF XY:

0.0325

AC XY:

2420

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.00786

Gnomad4 AMR

AF:

0.0251

Gnomad4 ASJ

AF:

0.0179

Gnomad4 EAS

AF:

0.114

Gnomad4 SAS

AF:

0.0508

Gnomad4 FIN

AF:

0.0210

Gnomad4 NFE

AF:

0.0441

Gnomad4 OTH

AF:

0.0317

Alfa

AF:

0.0382

Hom.:

Bravo

AF:

0.0317

Asia WGS

AF:

0.0680

AC:

236

AN:

3478

EpiCase

AF:

0.0433

EpiControl

AF:

0.0453

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:13

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:6

Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Aug 01, 2012	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Likely benign, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	-	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 15, 2015	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Tay-Sachs disease

Benign:4

Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jun 14, 2016	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jun 10, 2021	- -
Benign, no assertion criteria provided	clinical testing	Natera, Inc.	May 20, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jul 19, 2021	- -
Benign, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Dec 16, 2015	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Benign

0.93

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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