dbSNP rs755714: BAG6:c.2335+76G>A (chr6-31642036-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 NM_001387994.1(BAG6):c.2335+76G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 1,590,352 control chromosomes in the GnomAD database, including 73,234 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 0.24 ( 5582 hom., cov: 31)

Exomes 𝑓: 0.30 ( 67652 hom. )

Consequence

BAG6
NM_001387994.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.723

Publications

33 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001387994.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BAG6	NM_001387994.1	MANE Select	c.2335+76G>A	intron	N/A	NP_001374923.1	P46379-3
BAG6	NM_001388012.1		c.2362+76G>A	intron	N/A	NP_001374941.1
BAG6	NM_001387989.1		c.2335+76G>A	intron	N/A	NP_001374918.1	P46379-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BAG6	ENST00000676615.2	MANE Select	c.2335+76G>A	intron	N/A	ENSP00000502941.1	P46379-3
BAG6	ENST00000211379.9	TSL:1	c.2227+76G>A	intron	N/A	ENSP00000211379.5	P46379-2
BAG6	ENST00000375976.8	TSL:1	c.2227+76G>A	intron	N/A	ENSP00000365143.4	P46379-2

Frequencies

GnomAD3 genomes

AF:

0.240

AC:

36530

AN:

151898

Hom.:

5580

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0540

Gnomad AMI

AF:

0.345

Gnomad AMR

AF:

0.302

Gnomad ASJ

AF:

0.486

Gnomad EAS

AF:

0.360

Gnomad SAS

AF:

0.312

Gnomad FIN

AF:

0.283

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.267

GnomAD4 exome

AF:

0.299

AC:

430514

AN:

1438336

Hom.:

67652

Cov.:

AF XY:

0.303

AC XY:

215667

AN XY:

712556

show subpopulations

African (AFR)

AF:

0.0426

AC:

1404

AN:

32966

American (AMR)

AF:

0.375

AC:

16241

AN:

43282

Ashkenazi Jewish (ASJ)

AF:

0.484

AC:

11861

AN:

24508

East Asian (EAS)

AF:

0.418

AC:

16486

AN:

39426

South Asian (SAS)

AF:

0.308

AC:

25537

AN:

83002

European-Finnish (FIN)

AF:

0.281

AC:

14500

AN:

51518

Middle Eastern (MID)

AF:

0.390

AC:

2209

AN:

5658

European-Non Finnish (NFE)

AF:

0.296

AC:

325021

AN:

1098662

Other (OTH)

AF:

0.291

AC:

17255

AN:

59314

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

18384

36767

55151

73534

91918

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10654

21308

31962

42616

53270

<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:

0.240

AC:

36538

AN:

152016

Hom.:

5582

Cov.:

AF XY:

0.243

AC XY:

18075

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.0539

AC:

2239

AN:

41512

American (AMR)

AF:

0.302

AC:

4619

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.486

AC:

1685

AN:

3464

East Asian (EAS)

AF:

0.360

AC:

1856

AN:

5152

South Asian (SAS)

AF:

0.313

AC:

1510

AN:

4818

European-Finnish (FIN)

AF:

0.283

AC:

2983

AN:

10550

Middle Eastern (MID)

AF:

0.381

AC:

112

AN:

294

European-Non Finnish (NFE)

AF:

0.304

AC:

20658

AN:

67918

Other (OTH)

AF:

0.266

AC:

561

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1282

2564

3846

5128

6410

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

388

776

1164

1552

1940

<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:

0.284

Hom.:

19299

Bravo

AF:

0.234

Asia WGS

AF:

0.300

AC:

1047

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

8.2

(source)

DANN

Benign

0.56

PhyloP100

-0.72

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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