Genetic Variant ENST00000612409.1:n.248+1621A>G (chr6-33572432-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000612409.2(ENSG00000293518):n.248+1621A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,730 control chromosomes in the GnomAD database, including 39,825 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 0.72 ( 39648 hom., cov: 31)

Exomes 𝑓: 0.73 ( 177 hom. )

Consequence

ENSG00000293518
ENST00000612409.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.774

Publications

75 publications found

Variant links:

Genes affected

ENSG00000293518 (HGNC:):

ENSG00000293518 links:

BAK1 (HGNC:949): (BCL2 antagonist/killer 1) The protein encoded by this gene belongs to the BCL2 protein family. BCL2 family members form oligomers or heterodimers and act as anti- or pro-apoptotic regulators that are involved in a wide variety of cellular activities. This protein localizes to mitochondria, and functions to induce apoptosis. It interacts with and accelerates the opening of the mitochondrial voltage-dependent anion channel, which leads to a loss in membrane potential and the release of cytochrome c. This protein also interacts with the tumor suppressor P53 after exposure to cell stress. [provided by RefSeq, Jul 2008]

BAK1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000612409.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAK1	NM_001188.4	MANE Select	c.*1371T>C		downstream_gene	N/A	NP_001179.1	Q16611-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000293518	ENST00000612409.2	TSL:5	n.248+1621A>G	intron	N/A
ENSG00000293518	ENST00000738005.1		n.128+1621A>G	intron	N/A
ENSG00000293518	ENST00000738006.1		n.121+854A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.721

AC:

109613

AN:

151956

Hom.:

39610

Cov.:

show subpopulations

Gnomad AFR

AF:

0.722

Gnomad AMI

AF:

0.671

Gnomad AMR

AF:

0.723

Gnomad ASJ

AF:

0.765

Gnomad EAS

AF:

0.781

Gnomad SAS

AF:

0.729

Gnomad FIN

AF:

0.803

Gnomad MID

AF:

0.687

Gnomad NFE

AF:

0.702

Gnomad OTH

AF:

0.707

GnomAD4 exome

AF:

0.732

AC:

480

AN:

656

Hom.:

177

AF XY:

0.760

AC XY:

254

AN XY:

334

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.800

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.650

AC:

AN:

East Asian (EAS)

AF:

0.758

AC:

AN:

124

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.726

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.727

AC:

288

AN:

396

Other (OTH)

AF:

0.571

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.721

AC:

109704

AN:

152074

Hom.:

39648

Cov.:

AF XY:

0.725

AC XY:

53906

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.722

AC:

29950

AN:

41472

American (AMR)

AF:

0.723

AC:

11033

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.765

AC:

2655

AN:

3472

East Asian (EAS)

AF:

0.780

AC:

4033

AN:

5168

South Asian (SAS)

AF:

0.730

AC:

3518

AN:

4816

European-Finnish (FIN)

AF:

0.803

AC:

8509

AN:

10596

Middle Eastern (MID)

AF:

0.697

AC:

205

AN:

294

European-Non Finnish (NFE)

AF:

0.702

AC:

47709

AN:

67970

Other (OTH)

AF:

0.703

AC:

1480

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1570

3139

4709

6278

7848

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

840

1680

2520

3360

4200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.707

Hom.:

174181

Bravo

AF:

0.715

Asia WGS

AF:

0.701

AC:

2441

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

(source)

DANN

Benign

0.42

PhyloP100

0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over