Genetic Variant GBAP1:n.-249G>A (chr1-155227671-C-T) – 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.-249G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,094 control chromosomes in the GnomAD database, including 24,811 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 ( 24811 hom., cov: 34)

Consequence

GBAP1
ENST00000368374.5 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.394

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=-0.74).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GBA1LP	NR_002188.3 link	n.-137G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
GBAP1	ENST00000368374.5 link	n.-249G>A	upstream_gene_variant	1
GBAP1	ENST00000463838.6 link	n.-132G>A	upstream_gene_variant	2
GBAP1	ENST00000687347.1 link	n.-97G>A	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.566

AC:

86031

AN:

151976

Hom.:

24785

Cov.:

show subpopulations

Gnomad AFR

AF:

0.651

Gnomad AMI

AF:

0.366

Gnomad AMR

AF:

0.610

Gnomad ASJ

AF:

0.488

Gnomad EAS

AF:

0.778

Gnomad SAS

AF:

0.540

Gnomad FIN

AF:

0.548

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.501

Gnomad OTH

AF:

0.554

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.566

AC:

86098

AN:

152094

Hom.:

24811

Cov.:

AF XY:

0.568

AC XY:

42240

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.651

Gnomad4 AMR

AF:

0.610

Gnomad4 ASJ

AF:

0.488

Gnomad4 EAS

AF:

0.778

Gnomad4 SAS

AF:

0.538

Gnomad4 FIN

AF:

0.548

Gnomad4 NFE

AF:

0.501

Gnomad4 OTH

AF:

0.549

Alfa

AF:

0.518

Hom.:

10080

Bravo

AF:

0.580

Asia WGS

AF:

0.666

AC:

2317

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

0.39

DANN

Benign

0.67

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