Genetic Variant BAG6:c.918+69G>A (chr6-31646325-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000676615.2(BAG6):c.918+69G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 1,560,148 control chromosomes in the GnomAD database, including 497,819 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 0.76 ( 44043 hom., cov: 31)

Exomes 𝑓: 0.80 ( 453776 hom. )

Consequence

BAG6
ENST00000676615.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.50

Publications

39 publications found

Variant links:

Genes affected

BAG6 (HGNC:13919): (BAG cochaperone 6) This gene was first characterized as part of a cluster of genes located within the human major histocompatibility complex class III region. This gene encodes a nuclear protein that is cleaved by caspase 3 and is implicated in the control of apoptosis. In addition, the protein forms a complex with E1A binding protein p300 and is required for the acetylation of p53 in response to DNA damage. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

BAG6 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000676615.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BAG6	NM_001387994.1	MANE Select	c.918+69G>A	intron	N/A	NP_001374923.1
BAG6	NM_001388012.1		c.918+69G>A	intron	N/A	NP_001374941.1
BAG6	NM_001387989.1		c.918+69G>A	intron	N/A	NP_001374918.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BAG6	ENST00000676615.2	MANE Select	c.918+69G>A	intron	N/A	ENSP00000502941.1
BAG6	ENST00000211379.9	TSL:1	c.918+69G>A	intron	N/A	ENSP00000211379.5
BAG6	ENST00000375976.8	TSL:1	c.918+69G>A	intron	N/A	ENSP00000365143.4

Frequencies

GnomAD3 genomes

AF:

0.755

AC:

114702

AN:

151908

Hom.:

44002

Cov.:

show subpopulations

Gnomad AFR

AF:

0.612

Gnomad AMI

AF:

0.907

Gnomad AMR

AF:

0.787

Gnomad ASJ

AF:

0.761

Gnomad EAS

AF:

0.835

Gnomad SAS

AF:

0.818

Gnomad FIN

AF:

0.866

Gnomad MID

AF:

0.737

Gnomad NFE

AF:

0.805

Gnomad OTH

AF:

0.738

GnomAD4 exome

AF:

0.801

AC:

1128203

AN:

1408122

Hom.:

453776

AF XY:

0.802

AC XY:

558155

AN XY:

696092

show subpopulations

African (AFR)

AF:

0.608

AC:

19136

AN:

31452

American (AMR)

AF:

0.812

AC:

31377

AN:

38642

Ashkenazi Jewish (ASJ)

AF:

0.764

AC:

17919

AN:

23460

East Asian (EAS)

AF:

0.845

AC:

32143

AN:

38032

South Asian (SAS)

AF:

0.808

AC:

64813

AN:

80222

European-Finnish (FIN)

AF:

0.854

AC:

43086

AN:

50430

Middle Eastern (MID)

AF:

0.682

AC:

3746

AN:

5492

European-Non Finnish (NFE)

AF:

0.804

AC:

870793

AN:

1082530

Other (OTH)

AF:

0.781

AC:

45190

AN:

57862

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

11079

22158

33236

44315

55394

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20606

41212

61818

82424

103030

<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:

0.755

AC:

114789

AN:

152026

Hom.:

44043

Cov.:

AF XY:

0.759

AC XY:

56387

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.612

AC:

25342

AN:

41412

American (AMR)

AF:

0.788

AC:

12023

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.761

AC:

2640

AN:

3470

East Asian (EAS)

AF:

0.837

AC:

4335

AN:

5182

South Asian (SAS)

AF:

0.819

AC:

3948

AN:

4822

European-Finnish (FIN)

AF:

0.866

AC:

9175

AN:

10592

Middle Eastern (MID)

AF:

0.745

AC:

219

AN:

294

European-Non Finnish (NFE)

AF:

0.805

AC:

54720

AN:

67966

Other (OTH)

AF:

0.739

AC:

1560

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1372

2744

4115

5487

6859

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

858

1716

2574

3432

4290

<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:

0.790

Hom.:

183555

Bravo

AF:

0.743

Asia WGS

AF:

0.839

AC:

2918

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.49

(source)

DANN

Benign

0.80

PhyloP100

-1.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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