dbSNP rs10484558: BAG6:p.Thr214Thr (chr6-31647737-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001387994.1(BAG6):c.642A>G(p.Thr214Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0271 in 1,604,910 control chromosomes in the GnomAD database, including 1,326 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 0.052 ( 365 hom., cov: 31)

Exomes 𝑓: 0.025 ( 961 hom. )

Consequence

BAG6
NM_001387994.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.107

Publications

19 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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP7

Synonymous conserved (PhyloP=-0.107 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAG6	NM_001387994.1 link	c.642A>G	p.Thr214Thr	synonymous_variant	Exon 7 of 26	ENST00000676615.2	NP_001374923.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAG6	ENST00000676615.2 link	c.642A>G	p.Thr214Thr	synonymous_variant	Exon 7 of 26		NM_001387994.1	ENSP00000502941.1		P46379-3

Frequencies

GnomAD3 genomes

AF:

0.0515

AC:

7826

AN:

152104

Hom.:

361

Cov.:

show subpopulations

Gnomad AFR

AF:

0.111

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0574

Gnomad ASJ

AF:

0.141

Gnomad EAS

AF:

0.0169

Gnomad SAS

AF:

0.0180

Gnomad FIN

AF:

0.00198

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0220

Gnomad OTH

AF:

0.0750

GnomAD2 exomes

AF:

0.0339

AC:

8031

AN:

237004

AF XY:

0.0308

show subpopulations

Gnomad AFR exome

AF:

0.114

Gnomad AMR exome

AF:

0.0521

Gnomad ASJ exome

AF:

0.139

Gnomad EAS exome

AF:

0.0136

Gnomad FIN exome

AF:

0.00265

Gnomad NFE exome

AF:

0.0221

Gnomad OTH exome

AF:

0.0463

GnomAD4 exome

AF:

0.0245

AC:

35625

AN:

1452688

Hom.:

961

Cov.:

AF XY:

0.0243

AC XY:

17529

AN XY:

722836

show subpopulations

African (AFR)

AF:

0.110

AC:

3625

AN:

32856

American (AMR)

AF:

0.0532

AC:

2265

AN:

42572

Ashkenazi Jewish (ASJ)

AF:

0.139

AC:

3604

AN:

25854

East Asian (EAS)

AF:

0.0452

AC:

1772

AN:

39184

South Asian (SAS)

AF:

0.0162

AC:

1376

AN:

85038

European-Finnish (FIN)

AF:

0.00277

AC:

145

AN:

52298

Middle Eastern (MID)

AF:

0.0681

AC:

391

AN:

5742

European-Non Finnish (NFE)

AF:

0.0182

AC:

20160

AN:

1109060

Other (OTH)

AF:

0.0381

AC:

2287

AN:

60084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

2118

4237

6355

8474

10592

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

842

1684

2526

3368

4210

<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:

0.0516

AC:

7849

AN:

152222

Hom.:

365

Cov.:

AF XY:

0.0496

AC XY:

3693

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.111

AC:

4614

AN:

41504

American (AMR)

AF:

0.0574

AC:

878

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.141

AC:

488

AN:

3472

East Asian (EAS)

AF:

0.0170

AC:

AN:

5180

South Asian (SAS)

AF:

0.0176

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00198

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0220

AC:

1497

AN:

68018

Other (OTH)

AF:

0.0742

AC:

157

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

362

723

1085

1446

1808

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

234

312

390

<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:

0.0372

Hom.:

539

Bravo

AF:

0.0590

Asia WGS

AF:

0.0270

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

9.3

(source)

DANN

Benign

0.61

PhyloP100

-0.11

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.9

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over