Genetic Variant BAG6:c.2043+77T>C (chr6-31642752-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 NM_001387994.1(BAG6):c.2043+77T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 1,534,950 control chromosomes in the GnomAD database, including 184,268 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 0.45 ( 16023 hom., cov: 32)

Exomes 𝑓: 0.49 ( 168245 hom. )

Consequence

BAG6
NM_001387994.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.360

Publications

61 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAG6	NM_001387994.1 link	c.2043+77T>C		intron_variant	Intron 15 of 25	ENST00000676615.2	NP_001374923.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAG6	ENST00000676615.2 link	c.2043+77T>C		intron_variant	Intron 15 of 25		NM_001387994.1	ENSP00000502941.1		P46379-3

Frequencies

GnomAD3 genomes

AF:

0.450

AC:

68389

AN:

151972

Hom.:

16004

Cov.:

show subpopulations

Gnomad AFR

AF:

0.337

Gnomad AMI

AF:

0.598

Gnomad AMR

AF:

0.500

Gnomad ASJ

AF:

0.616

Gnomad EAS

AF:

0.607

Gnomad SAS

AF:

0.588

Gnomad FIN

AF:

0.374

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.486

Gnomad OTH

AF:

0.480

GnomAD4 exome

AF:

0.490

AC:

677463

AN:

1382860

Hom.:

168245

Cov.:

AF XY:

0.495

AC XY:

341133

AN XY:

688558

show subpopulations

African (AFR)

AF:

0.333

AC:

10085

AN:

30322

American (AMR)

AF:

0.507

AC:

20814

AN:

41028

Ashkenazi Jewish (ASJ)

AF:

0.613

AC:

15362

AN:

25054

East Asian (EAS)

AF:

0.584

AC:

20953

AN:

35852

South Asian (SAS)

AF:

0.589

AC:

47568

AN:

80820

European-Finnish (FIN)

AF:

0.380

AC:

17298

AN:

45512

Middle Eastern (MID)

AF:

0.539

AC:

2918

AN:

5412

European-Non Finnish (NFE)

AF:

0.484

AC:

514188

AN:

1061502

Other (OTH)

AF:

0.493

AC:

28277

AN:

57358

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

18431

36861

55292

73722

92153

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.450

AC:

68452

AN:

152090

Hom.:

16023

Cov.:

AF XY:

0.450

AC XY:

33423

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.337

AC:

14002

AN:

41490

American (AMR)

AF:

0.499

AC:

7639

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.616

AC:

2137

AN:

3470

East Asian (EAS)

AF:

0.608

AC:

3138

AN:

5162

South Asian (SAS)

AF:

0.588

AC:

2835

AN:

4820

European-Finnish (FIN)

AF:

0.374

AC:

3955

AN:

10582

Middle Eastern (MID)

AF:

0.527

AC:

155

AN:

294

European-Non Finnish (NFE)

AF:

0.486

AC:

33026

AN:

67958

Other (OTH)

AF:

0.484

AC:

1021

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1914

3828

5742

7656

9570

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.476

Hom.:

55696

Bravo

AF:

0.452

Asia WGS

AF:

0.597

AC:

2079

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.64

(source)

DANN

Benign

0.66

PhyloP100

-0.36

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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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6-31642752-A-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over