dbSNP rs704243: BAX:c.*78G>A (chr19-48961714-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_138761.4(BAX):c.*78G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.894 in 1,067,090 control chromosomes in the GnomAD database, including 428,073 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 0.89 ( 59164 hom., cov: 23)

Exomes 𝑓: 0.89 ( 368909 hom. )

Consequence

BAX
NM_138761.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.398

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAX	NM_138761.4 link	c.*78G>A		3_prime_UTR_variant	Exon 6 of 6	ENST00000345358.12	NP_620116.1	Q07812-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAX	ENST00000345358.12 link	c.*78G>A		3_prime_UTR_variant	Exon 6 of 6	1	NM_138761.4	ENSP00000263262.9		Q07812-1

Frequencies

GnomAD3 genomes

AF:

0.889

AC:

132878

AN:

149496

Hom.:

59118

Cov.:

show subpopulations

Gnomad AFR

AF:

0.894

Gnomad AMI

AF:

0.856

Gnomad AMR

AF:

0.853

Gnomad ASJ

AF:

0.918

Gnomad EAS

AF:

0.932

Gnomad SAS

AF:

0.937

Gnomad FIN

AF:

0.903

Gnomad MID

AF:

0.904

Gnomad NFE

AF:

0.884

Gnomad OTH

AF:

0.877

GnomAD4 exome

AF:

0.895

AC:

820996

AN:

917478

Hom.:

368909

Cov.:

AF XY:

0.897

AC XY:

416464

AN XY:

464466

show subpopulations

Gnomad4 AFR exome

AF:

0.892

Gnomad4 AMR exome

AF:

0.836

Gnomad4 ASJ exome

AF:

0.923

Gnomad4 EAS exome

AF:

0.951

Gnomad4 SAS exome

AF:

0.935

Gnomad4 FIN exome

AF:

0.909

Gnomad4 NFE exome

AF:

0.889

Gnomad4 OTH exome

AF:

0.894

GnomAD4 genome

AF:

0.889

AC:

132980

AN:

149612

Hom.:

59164

Cov.:

AF XY:

0.890

AC XY:

64915

AN XY:

72942

show subpopulations

Gnomad4 AFR

AF:

0.894

Gnomad4 AMR

AF:

0.854

Gnomad4 ASJ

AF:

0.918

Gnomad4 EAS

AF:

0.932

Gnomad4 SAS

AF:

0.937

Gnomad4 FIN

AF:

0.903

Gnomad4 NFE

AF:

0.884

Gnomad4 OTH

AF:

0.877

Alfa

AF:

0.882

Hom.:

12216

Bravo

AF:

0.884

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

7.5

DANN

Benign

0.89

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.0

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.

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