1-155239569-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000157.4(GBA1):​c.454+47G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 1,608,550 control chromosomes in the GnomAD database, including 95,559 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 14392 hom., cov: 31)
Exomes 𝑓: 0.32 ( 81167 hom. )

Consequence

GBA1
NM_000157.4 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -2.42
Variant links:
Genes affected
GBA1 (HGNC:4177): (glucosylceramidase beta 1) This gene encodes a lysosomal membrane protein that cleaves the beta-glucosidic linkage of glycosylceramide, an intermediate in glycolipid metabolism. Mutations in this gene cause Gaucher disease, a lysosomal storage disease characterized by an accumulation of glucocerebrosides. A related pseudogene is approximately 12 kb downstream of this gene on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2010]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
Variant 1-155239569-C-T is Benign according to our data. Variant chr1-155239569-C-T is described in ClinVar as [Benign]. Clinvar id is 256873.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GBA1NM_000157.4 linkc.454+47G>A intron_variant ENST00000368373.8 NP_000148.2 P04062-1A0A068F658

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GBA1ENST00000368373.8 linkc.454+47G>A intron_variant 1 NM_000157.4 ENSP00000357357.3 P04062-1

Frequencies

GnomAD3 genomes
AF:
0.408
AC:
61998
AN:
151820
Hom.:
14346
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.616
Gnomad AMI
AF:
0.134
Gnomad AMR
AF:
0.359
Gnomad ASJ
AF:
0.295
Gnomad EAS
AF:
0.705
Gnomad SAS
AF:
0.358
Gnomad FIN
AF:
0.326
Gnomad MID
AF:
0.288
Gnomad NFE
AF:
0.298
Gnomad OTH
AF:
0.384
GnomAD3 exomes
AF:
0.367
AC:
90926
AN:
247432
Hom.:
18697
AF XY:
0.357
AC XY:
47844
AN XY:
134170
show subpopulations
Gnomad AFR exome
AF:
0.629
Gnomad AMR exome
AF:
0.403
Gnomad ASJ exome
AF:
0.301
Gnomad EAS exome
AF:
0.706
Gnomad SAS exome
AF:
0.352
Gnomad FIN exome
AF:
0.321
Gnomad NFE exome
AF:
0.286
Gnomad OTH exome
AF:
0.339
GnomAD4 exome
AF:
0.321
AC:
467210
AN:
1456612
Hom.:
81167
Cov.:
32
AF XY:
0.319
AC XY:
231011
AN XY:
724818
show subpopulations
Gnomad4 AFR exome
AF:
0.623
Gnomad4 AMR exome
AF:
0.401
Gnomad4 ASJ exome
AF:
0.302
Gnomad4 EAS exome
AF:
0.727
Gnomad4 SAS exome
AF:
0.345
Gnomad4 FIN exome
AF:
0.312
Gnomad4 NFE exome
AF:
0.292
Gnomad4 OTH exome
AF:
0.342
GnomAD4 genome
AF:
0.409
AC:
62091
AN:
151938
Hom.:
14392
Cov.:
31
AF XY:
0.406
AC XY:
30186
AN XY:
74266
show subpopulations
Gnomad4 AFR
AF:
0.617
Gnomad4 AMR
AF:
0.360
Gnomad4 ASJ
AF:
0.295
Gnomad4 EAS
AF:
0.704
Gnomad4 SAS
AF:
0.356
Gnomad4 FIN
AF:
0.326
Gnomad4 NFE
AF:
0.297
Gnomad4 OTH
AF:
0.381
Alfa
AF:
0.329
Hom.:
3596
Bravo
AF:
0.425
Asia WGS
AF:
0.563
AC:
1960
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:2
Benign, criteria provided, single submitterclinical testingUnidad de Genómica Garrahan, Hospital de Pediatría GarrahanJul 31, 2024This variant is classified as Benign based on local population frequency. This variant was detected in 54% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy, Progressive Myoclonus Epilepsy and Abnormal Movements and Neurodegeneration with brain iron accumulation. Number of patients: 50. Only high quality variants are reported. -
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
Gaucher disease type I Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabJul 01, 2021- -
Gaucher disease perinatal lethal Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabJul 01, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.086
DANN
Benign
0.62

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.

Other links and lift over

dbSNP: rs2075569; hg19: chr1-155209360; API