Genetic Variant GBAP1:n.42-102A>G (chr1-155225189-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000368374.5(GBAP1):n.42-102A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 224,830 control chromosomes in the GnomAD database, including 37,909 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.57 ( 25025 hom., cov: 33)

Exomes 𝑓: 0.58 ( 12884 hom. )

Consequence

GBAP1
ENST00000368374.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.580

Variant links:

Genes affected

GBAP1 (HGNC:):

GBAP1 links:

GBA1LP (HGNC:4178): (glucosylceramidase beta 1 like, pseudogene)

GBA1LP links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GBA1LP	NR_002188.3 link	n.153+2193A>G		intron_variant	Intron 1 of 12

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
GBAP1	ENST00000368374.5 link	n.42-102A>G	intron_variant	Intron 1 of 10	1
GBAP1	ENST00000463838.6 link	n.158+2193A>G	intron_variant	Intron 1 of 9	2
GBAP1	ENST00000688506.1 link	n.81+2193A>G	intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes

AF:

0.568

AC:

86341

AN:

151876

Hom.:

24986

Cov.:

show subpopulations

Gnomad AFR

AF:

0.653

Gnomad AMI

AF:

0.368

Gnomad AMR

AF:

0.613

Gnomad ASJ

AF:

0.481

Gnomad EAS

AF:

0.778

Gnomad SAS

AF:

0.539

Gnomad FIN

AF:

0.548

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.505

Gnomad OTH

AF:

0.557

GnomAD4 exome

AF:

0.583

AC:

42485

AN:

72836

Hom.:

12884

AF XY:

0.582

AC XY:

23431

AN XY:

40236

show subpopulations

Gnomad4 AFR exome

AF:

0.701

Gnomad4 AMR exome

AF:

0.665

Gnomad4 ASJ exome

AF:

0.494

Gnomad4 EAS exome

AF:

0.790

Gnomad4 SAS exome

AF:

0.570

Gnomad4 FIN exome

AF:

0.582

Gnomad4 NFE exome

AF:

0.533

Gnomad4 OTH exome

AF:

0.574

GnomAD4 genome

AF:

0.569

AC:

86427

AN:

151994

Hom.:

25025

Cov.:

AF XY:

0.570

AC XY:

42368

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.654

Gnomad4 AMR

AF:

0.613

Gnomad4 ASJ

AF:

0.481

Gnomad4 EAS

AF:

0.777

Gnomad4 SAS

AF:

0.538

Gnomad4 FIN

AF:

0.548

Gnomad4 NFE

AF:

0.505

Gnomad4 OTH

AF:

0.552

Alfa

AF:

0.516

Hom.:

40777

Bravo

AF:

0.583

Asia WGS

AF:

0.669

AC:

2328

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

1.6

DANN

Benign

0.77

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over