Genetic Variant NM_001387994.1:c.1669-23A>G (chr6-31644000-T-C) – 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.1669-23A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 1,613,678 control chromosomes in the GnomAD database, including 550,293 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 0.81 ( 49963 hom., cov: 31)

Exomes 𝑓: 0.83 ( 500330 hom. )

Consequence

BAG6
NM_001387994.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.80

Publications

31 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 = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAG6	NM_001387994.1 link	c.1669-23A>G		intron_variant	Intron 13 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.1669-23A>G		intron_variant	Intron 13 of 25		NM_001387994.1	ENSP00000502941.1		P46379-3

Frequencies

GnomAD3 genomes

AF:

0.809

AC:

122901

AN:

151980

Hom.:

49908

Cov.:

show subpopulations

Gnomad AFR

AF:

0.729

Gnomad AMI

AF:

0.910

Gnomad AMR

AF:

0.845

Gnomad ASJ

AF:

0.901

Gnomad EAS

AF:

0.853

Gnomad SAS

AF:

0.837

Gnomad FIN

AF:

0.870

Gnomad MID

AF:

0.794

Gnomad NFE

AF:

0.827

Gnomad OTH

AF:

0.815

GnomAD2 exomes

AF:

0.838

AC:

209298

AN:

249740

AF XY:

0.837

show subpopulations

Gnomad AFR exome

AF:

0.728

Gnomad AMR exome

AF:

0.874

Gnomad ASJ exome

AF:

0.909

Gnomad EAS exome

AF:

0.848

Gnomad FIN exome

AF:

0.863

Gnomad NFE exome

AF:

0.834

Gnomad OTH exome

AF:

0.839

GnomAD4 exome

AF:

0.826

AC:

1207749

AN:

1461580

Hom.:

500330

Cov.:

AF XY:

0.827

AC XY:

601090

AN XY:

727116

show subpopulations

African (AFR)

AF:

0.727

AC:

24325

AN:

33476

American (AMR)

AF:

0.870

AC:

38877

AN:

44698

Ashkenazi Jewish (ASJ)

AF:

0.904

AC:

23598

AN:

26116

East Asian (EAS)

AF:

0.890

AC:

35314

AN:

39692

South Asian (SAS)

AF:

0.823

AC:

70985

AN:

86246

European-Finnish (FIN)

AF:

0.858

AC:

45805

AN:

53400

Middle Eastern (MID)

AF:

0.752

AC:

4338

AN:

5768

European-Non Finnish (NFE)

AF:

0.823

AC:

914990

AN:

1111810

Other (OTH)

AF:

0.820

AC:

49517

AN:

60374

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

12586

25173

37759

50346

62932

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.809

AC:

123013

AN:

152098

Hom.:

49963

Cov.:

AF XY:

0.810

AC XY:

60250

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.729

AC:

30231

AN:

41448

American (AMR)

AF:

0.846

AC:

12931

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.901

AC:

3130

AN:

3472

East Asian (EAS)

AF:

0.854

AC:

4416

AN:

5170

South Asian (SAS)

AF:

0.837

AC:

4032

AN:

4820

European-Finnish (FIN)

AF:

0.870

AC:

9234

AN:

10608

Middle Eastern (MID)

AF:

0.806

AC:

237

AN:

294

European-Non Finnish (NFE)

AF:

0.827

AC:

56246

AN:

67972

Other (OTH)

AF:

0.816

AC:

1726

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1197

2394

3592

4789

5986

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.828

Hom.:

196697

Bravo

AF:

0.805

Asia WGS

AF:

0.870

AC:

3026

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

0.31

(source)

DANN

Benign

0.42

PhyloP100

-1.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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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NM_001387994.1:c.1669-23A>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