Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000404.4(GLB1):c.1824G>C(p.Leu608Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0202 in 1,614,126 control chromosomes in the GnomAD database, including 4,368 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.022 ( 508 hom., cov: 32)

Exomes 𝑓: 0.020 ( 3860 hom. )

Consequence

GLB1
NM_000404.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: 0.172

Publications

14 publications found

Variant links:

Genes affected

GLB1 (HGNC:4298): (galactosidase beta 1) This gene encodes a member of the glycosyl hydrolase 35 family of proteins. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature lysosomal enzyme. This enzyme catalyzes the hydrolysis of a terminal beta-linked galactose residue from ganglioside substrates and other glycoconjugates. Mutations in this gene may result in GM1-gangliosidosis and Morquio B syndrome. [provided by RefSeq, Nov 2015]

GLB1 Gene-Disease associations (from GenCC):

GM1 gangliosidosis
Inheritance: AR Classification: DEFINITIVE Submitted by: Myriad Women’s Health, ClinGen
GM1 gangliosidosis type 3
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp
mucopolysaccharidosis type 4B
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
GM1 gangliosidosis type 1
Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet
GM1 gangliosidosis type 2
Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp

GLB1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 3-32997255-C-G is Benign according to our data. Variant chr3-32997255-C-G is described in ClinVar as Benign. ClinVar VariationId is 92902.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.172 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000404.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
GLB1	NM_000404.4	MANE Select	c.1824G>C	p.Leu608Leu	synonymous	Exon 16 of 16	NP_000395.3
GLB1	NM_001317040.2		c.1968G>C	p.Leu656Leu	synonymous	Exon 17 of 17	NP_001303969.2
GLB1	NM_001079811.3		c.1734G>C	p.Leu578Leu	synonymous	Exon 16 of 16	NP_001073279.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
GLB1	ENST00000307363.10	TSL:1 MANE Select	c.1824G>C	p.Leu608Leu	synonymous	Exon 16 of 16	ENSP00000306920.4
GLB1	ENST00000307377.12	TSL:1	c.1431G>C	p.Leu477Leu	synonymous	Exon 13 of 13	ENSP00000305920.8
GLB1	ENST00000399402.7	TSL:2	c.1734G>C	p.Leu578Leu	synonymous	Exon 16 of 16	ENSP00000382333.2

Frequencies

GnomAD3 genomes

AF:

0.0219

AC:

3333

AN:

152118

Hom.:

514

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00345

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.00432

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.419

Gnomad SAS

AF:

0.0976

Gnomad FIN

AF:

0.0235

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00279

Gnomad OTH

AF:

0.0206

GnomAD2 exomes

AF:

0.0458

AC:

11430

AN:

249464

AF XY:

0.0466

show subpopulations

Gnomad AFR exome

AF:

0.00303

Gnomad AMR exome

AF:

0.00258

Gnomad ASJ exome

AF:

0.00298

Gnomad EAS exome

AF:

0.423

Gnomad FIN exome

AF:

0.0246

Gnomad NFE exome

AF:

0.00279

Gnomad OTH exome

AF:

0.0248

GnomAD4 exome

AF:

0.0200

AC:

29207

AN:

1461890

Hom.:

3860

Cov.:

AF XY:

0.0221

AC XY:

16038

AN XY:

727246

show subpopulations

African (AFR)

AF:

0.00179

AC:

AN:

33480

American (AMR)

AF:

0.00235

AC:

105

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00241

AC:

AN:

26136

East Asian (EAS)

AF:

0.405

AC:

16083

AN:

39700

South Asian (SAS)

AF:

0.0864

AC:

7454

AN:

86258

European-Finnish (FIN)

AF:

0.0250

AC:

1336

AN:

53420

Middle Eastern (MID)

AF:

0.00434

AC:

AN:

5764

European-Non Finnish (NFE)

AF:

0.00208

AC:

2315

AN:

1112012

Other (OTH)

AF:

0.0292

AC:

1766

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1681

3361

5042

6722

8403

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

376

752

1128

1504

1880

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0218

AC:

3326

AN:

152236

Hom.:

508

Cov.:

AF XY:

0.0263

AC XY:

1955

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.00344

AC:

143

AN:

41550

American (AMR)

AF:

0.00431

AC:

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.00317

AC:

AN:

3472

East Asian (EAS)

AF:

0.418

AC:

2147

AN:

5140

South Asian (SAS)

AF:

0.0974

AC:

470

AN:

4824

European-Finnish (FIN)

AF:

0.0235

AC:

249

AN:

10602

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00279

AC:

190

AN:

68036

Other (OTH)

AF:

0.0228

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

111

222

332

443

554

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

162

216

270

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00624

Hom.:

Bravo

AF:

0.0198

Asia WGS

AF:

0.192

AC:

664

AN:

3478

EpiCase

AF:

0.00251

EpiControl

AF:

0.00184

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

Mucopolysaccharidosis, MPS-IV-B (2)

not specified (2)

GM1 gangliosidosis (1)

GM1 gangliosidosis;C0086652:Mucopolysaccharidosis, MPS-IV-B (1)

Infantile GM1 gangliosidosis (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

7.2

(source)

DANN

Benign

0.45

PhyloP100

0.17

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

rs77226678

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

ClinVar submissions as Germline

Computational scores

Splicing

Publications

Other links and lift over