Variant rs1805419 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_138761.4(BAX):c.233+14A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 1,563,434 control chromosomes in the GnomAD database, including 385,281 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.66 ( 33385 hom., cov: 28)

Exomes 𝑓: 0.70 ( 351896 hom. )

Consequence

BAX
NM_138761.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.973

Variant links:

Genes affected

BAX (HGNC:959): (BCL2 associated X, apoptosis regulator) The protein encoded by this gene belongs to the BCL2 protein family. BCL2 family members form hetero- or homodimers and act as anti- or pro-apoptotic regulators that are involved in a wide variety of cellular activities. This protein forms a heterodimer with BCL2, and functions as an apoptotic activator. The association and the ratio of BAX to BCL2 also determines survival or death of a cell following an apoptotic stimulus. This protein is reported to interact with, and increase the opening of, the mitochondrial voltage-dependent anion channel (VDAC), which leads to the loss in membrane potential and the release of cytochrome c. The expression of this gene is regulated by the tumor suppressor P53 and has been shown to be involved in P53-mediated apoptosis. Multiple alternatively spliced transcript variants, which encode different isoforms, have been reported for this gene. [provided by RefSeq, Dec 2019]

BAX links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 19-48955847-A-G is Benign according to our data. Variant chr19-48955847-A-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAX	NM_138761.4 linkuse as main transcript	c.233+14A>G		intron_variant		ENST00000345358.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAX	ENST00000345358.12 linkuse as main transcript	c.233+14A>G		intron_variant		1	NM_138761.4	P1	Q07812-1

Frequencies

GnomAD3 genomes

AF:

0.662

AC:

100105

AN:

151304

Hom.:

33376

Cov.:

show subpopulations

Gnomad AFR

AF:

0.583

Gnomad AMI

AF:

0.680

Gnomad AMR

AF:

0.630

Gnomad ASJ

AF:

0.827

Gnomad EAS

AF:

0.595

Gnomad SAS

AF:

0.647

Gnomad FIN

AF:

0.627

Gnomad MID

AF:

0.755

Gnomad NFE

AF:

0.718

Gnomad OTH

AF:

0.664

GnomAD3 exomes

AF:

0.671

AC:

145099

AN:

216292

Hom.:

49311

AF XY:

0.678

AC XY:

79239

AN XY:

116798

show subpopulations

Gnomad AFR exome

AF:

0.584

Gnomad AMR exome

AF:

0.574

Gnomad ASJ exome

AF:

0.831

Gnomad EAS exome

AF:

0.595

Gnomad SAS exome

AF:

0.659

Gnomad FIN exome

AF:

0.642

Gnomad NFE exome

AF:

0.720

Gnomad OTH exome

AF:

0.704

GnomAD4 exome

AF:

0.704

AC:

994305

AN:

1412012

Hom.:

351896

Cov.:

AF XY:

0.705

AC XY:

491923

AN XY:

697676

show subpopulations

Gnomad4 AFR exome

AF:

0.585

Gnomad4 AMR exome

AF:

0.578

Gnomad4 ASJ exome

AF:

0.831

Gnomad4 EAS exome

AF:

0.643

Gnomad4 SAS exome

AF:

0.658

Gnomad4 FIN exome

AF:

0.646

Gnomad4 NFE exome

AF:

0.718

Gnomad4 OTH exome

AF:

0.696

GnomAD4 genome

AF:

0.661

AC:

100143

AN:

151422

Hom.:

33385

Cov.:

AF XY:

0.656

AC XY:

48504

AN XY:

73940

show subpopulations

Gnomad4 AFR

AF:

0.583

Gnomad4 AMR

AF:

0.630

Gnomad4 ASJ

AF:

0.827

Gnomad4 EAS

AF:

0.595

Gnomad4 SAS

AF:

0.647

Gnomad4 FIN

AF:

0.627

Gnomad4 NFE

AF:

0.718

Gnomad4 OTH

AF:

0.665

Alfa

AF:

0.710

Hom.:

51774

Bravo

AF:

0.659

Asia WGS

AF:

0.561

AC:

1955

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

2.4

DANN

Benign

0.70

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over