5-74685474-C-T

Position:

chr5-74685474-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_000521.4(HEXB):c.214C>T(p.Leu72Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0101 in 1,611,790 control chromosomes in the GnomAD database, including 113 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L72L) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0076 ( 4 hom., cov: 30)

Exomes 𝑓: 0.010 ( 109 hom. )

Consequence

HEXB
NM_000521.4 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: 0.330

Variant links:

Genes affected

HEXB (HGNC:4879): (hexosaminidase subunit beta) Hexosaminidase B is the beta subunit of the lysosomal enzyme beta-hexosaminidase that, together with the cofactor GM2 activator protein, catalyzes the degradation of the ganglioside GM2, and other molecules containing terminal N-acetyl hexosamines. Beta-hexosaminidase is composed of two subunits, alpha and beta, which are encoded by separate genes. Both beta-hexosaminidase alpha and beta subunits are members of family 20 of glycosyl hydrolases. Mutations in the alpha or beta subunit genes lead to an accumulation of GM2 ganglioside in neurons and neurodegenerative disorders termed the GM2 gangliosidoses. Beta subunit gene mutations lead to Sandhoff disease (GM2-gangliosidosis type II). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2014]

HEXB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005268872).

BP6

Variant 5-74685474-C-T is Benign according to our data. Variant chr5-74685474-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 129224.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-74685474-C-T is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00763 (1160/151966) while in subpopulation NFE AF= 0.0104 (706/67936). AF 95% confidence interval is 0.00976. There are 4 homozygotes in gnomad4. There are 554 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HEXB	NM_000521.4 linkuse as main transcript	c.214C>T	p.Leu72Phe	missense_variant	1/14	ENST00000261416.12
HEXB	NM_001292004.2 linkuse as main transcript	c.-376-3854C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
HEXB	ENST00000261416.12 linkuse as main transcript	c.214C>T	p.Leu72Phe	missense_variant	1/14	1	NM_000521.4	P1
HEXB	ENST00000511181.5 linkuse as main transcript	c.-376-3854C>T		intron_variant		1
HEXB	ENST00000513079.5 linkuse as main transcript	n.279C>T		non_coding_transcript_exon_variant	1/6	2
HEXB	ENST00000515528.1 linkuse as main transcript	n.269C>T		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes

AF:

0.00764

AC:

1160

AN:

151848

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00215

Gnomad AMI

AF:

0.0439

Gnomad AMR

AF:

0.00675

Gnomad ASJ

AF:

0.0156

Gnomad EAS

AF:

0.000974

Gnomad SAS

AF:

0.00945

Gnomad FIN

AF:

0.00943

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0104

Gnomad OTH

AF:

0.00817

GnomAD3 exomes

AF:

0.00776

AC:

1903

AN:

245082

Hom.:

AF XY:

0.00791

AC XY:

1056

AN XY:

133488

show subpopulations

Gnomad AFR exome

AF:

0.00191

Gnomad AMR exome

AF:

0.00488

Gnomad ASJ exome

AF:

0.0142

Gnomad EAS exome

AF:

0.0000558

Gnomad SAS exome

AF:

0.00768

Gnomad FIN exome

AF:

0.00777

Gnomad NFE exome

AF:

0.0100

Gnomad OTH exome

AF:

0.0107

GnomAD4 exome

AF:

0.0103

AC:

15074

AN:

1459824

Hom.:

109

Cov.:

AF XY:

0.0102

AC XY:

7431

AN XY:

726230

show subpopulations

Gnomad4 AFR exome

AF:

0.00183

Gnomad4 AMR exome

AF:

0.00551

Gnomad4 ASJ exome

AF:

0.0125

Gnomad4 EAS exome

AF:

0.0000505

Gnomad4 SAS exome

AF:

0.00827

Gnomad4 FIN exome

AF:

0.00903

Gnomad4 NFE exome

AF:

0.0114

Gnomad4 OTH exome

AF:

0.00952

GnomAD4 genome

AF:

0.00763

AC:

1160

AN:

151966

Hom.:

Cov.:

AF XY:

0.00746

AC XY:

554

AN XY:

74266

show subpopulations

Gnomad4 AFR

AF:

0.00214

Gnomad4 AMR

AF:

0.00674

Gnomad4 ASJ

AF:

0.0156

Gnomad4 EAS

AF:

0.00117

Gnomad4 SAS

AF:

0.00946

Gnomad4 FIN

AF:

0.00943

Gnomad4 NFE

AF:

0.0104

Gnomad4 OTH

AF:

0.00808

Alfa

AF:

0.0100

Hom.:

Bravo

AF:

0.00738

TwinsUK

AF:

0.00998

AC:

ALSPAC

AF:

0.0145

AC:

ESP6500AA

AF:

0.00340

AC:

ESP6500EA

AF:

0.0112

AC:

ExAC

AF:

0.00745

AC:

904

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.0106

EpiControl

AF:

0.00856

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Benign, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Oct 23, 2015	- -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2024	HEXB: BS1, BS2 -
Likely benign, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Feb 17, 2016	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 25, 2019	- -

Sandhoff disease

Benign:3

Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Dec 04, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	May 01, 2017	- -
Likely benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Apr 22, 2016	- -

HEXB-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 15, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.36

CADD

Benign

DANN

Uncertain

0.99

Eigen

Benign

-0.35

Eigen_PC

Benign

-0.61

FATHMM_MKL

Benign

0.018

MetaRNN

Benign

0.0053

MetaSVM

Uncertain

-0.12

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.41

PROVEAN

Uncertain

-2.8

REVEL

Uncertain

0.31

Sift

Uncertain

0.0050

Sift4G

Uncertain

0.053

Vest4

0.22

MVP

0.82

MPC

0.49

ClinPred

0.039

GERP RS

-0.56

gMVP

0.76

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