Genetic Variant BAG6:c.552+88C>T (chr6-31648589-G-A) – 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.552+88C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 1,298,384 control chromosomes in the GnomAD database, including 100,027 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 0.44 ( 15683 hom., cov: 31)

Exomes 𝑓: 0.38 ( 84344 hom. )

Consequence

BAG6
NM_001387994.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.224

Publications

116 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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.552+88C>T	intron	N/A	NP_001374923.1	P46379-3
BAG6	NM_001388012.1		c.552+88C>T	intron	N/A	NP_001374941.1
BAG6	NM_001387989.1		c.552+88C>T	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.552+88C>T	intron	N/A	ENSP00000502941.1	P46379-3
BAG6	ENST00000211379.9	TSL:1	c.552+88C>T	intron	N/A	ENSP00000211379.5	P46379-2
BAG6	ENST00000375976.8	TSL:1	c.552+88C>T	intron	N/A	ENSP00000365143.4	P46379-2

Frequencies

GnomAD3 genomes

AF:

0.444

AC:

67418

AN:

151802

Hom.:

15668

Cov.:

show subpopulations

Gnomad AFR

AF:

0.592

Gnomad AMI

AF:

0.331

Gnomad AMR

AF:

0.422

Gnomad ASJ

AF:

0.336

Gnomad EAS

AF:

0.384

Gnomad SAS

AF:

0.310

Gnomad FIN

AF:

0.502

Gnomad MID

AF:

0.414

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.431

GnomAD4 exome

AF:

0.378

AC:

433619

AN:

1146464

Hom.:

84344

AF XY:

0.372

AC XY:

214941

AN XY:

578074

show subpopulations

African (AFR)

AF:

0.603

AC:

16000

AN:

26530

American (AMR)

AF:

0.429

AC:

16201

AN:

37780

Ashkenazi Jewish (ASJ)

AF:

0.341

AC:

7317

AN:

21458

East Asian (EAS)

AF:

0.414

AC:

15563

AN:

37636

South Asian (SAS)

AF:

0.288

AC:

21335

AN:

74116

European-Finnish (FIN)

AF:

0.481

AC:

24714

AN:

51408

Middle Eastern (MID)

AF:

0.326

AC:

1165

AN:

3570

European-Non Finnish (NFE)

AF:

0.370

AC:

312369

AN:

844708

Other (OTH)

AF:

0.385

AC:

18955

AN:

49258

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

13582

27164

40747

54329

67911

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9152

18304

27456

36608

45760

<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:

0.444

AC:

67474

AN:

151920

Hom.:

15683

Cov.:

AF XY:

0.446

AC XY:

33116

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.592

AC:

24510

AN:

41432

American (AMR)

AF:

0.423

AC:

6457

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.336

AC:

1165

AN:

3468

East Asian (EAS)

AF:

0.384

AC:

1980

AN:

5162

South Asian (SAS)

AF:

0.310

AC:

1490

AN:

4810

European-Finnish (FIN)

AF:

0.502

AC:

5299

AN:

10554

Middle Eastern (MID)

AF:

0.411

AC:

120

AN:

292

European-Non Finnish (NFE)

AF:

0.372

AC:

25248

AN:

67916

Other (OTH)

AF:

0.430

AC:

904

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1859

3718

5576

7435

9294

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

600

1200

1800

2400

3000

<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:

0.395

Hom.:

49656

Bravo

AF:

0.449

Asia WGS

AF:

0.363

AC:

1262

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.0

(source)

DANN

Benign

0.29

PhyloP100

-0.22

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