Genetic Variant DNAJB9:p.Pro61Pro (chr7-108571909-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

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

The NM_012328.3(DNAJB9):c.183G>A(p.Pro61Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 1,613,686 control chromosomes in the GnomAD database, including 218,132 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 0.46 ( 17286 hom., cov: 32)

Exomes 𝑓: 0.52 ( 200846 hom. )

Consequence

DNAJB9
NM_012328.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.206

Publications

27 publications found

Variant links:

Genes affected

DNAJB9 (HGNC:6968): (DnaJ heat shock protein family (Hsp40) member B9) This gene is a member of the J protein family. J proteins function in many cellular processes by regulating the ATPase activity of 70 kDa heat shock proteins. This gene is a member of the type 2 subgroup of DnaJ proteins. The encoded protein is localized to the endoplasmic reticulum. This protein is induced by endoplasmic reticulum stress and plays a role in protecting stressed cells from apoptosis. [provided by RefSeq, Dec 2010]

DNAJB9 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=-0.5).

BP7

Synonymous conserved (PhyloP=0.206 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJB9	NM_012328.3 link	c.183G>A	p.Pro61Pro	synonymous_variant	Exon 2 of 3	ENST00000249356.4	NP_036460.1	Q9UBS3Q6FIF1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
DNAJB9	ENST00000249356.4 link	c.183G>A	p.Pro61Pro	synonymous_variant	Exon 2 of 3	1	NM_012328.3	ENSP00000249356.3	Q9UBS3
DNAJB9	ENST00000465725.1 link	n.195G>A		non_coding_transcript_exon_variant	Exon 1 of 2	2
DNAJB9	ENST00000491582.1 link	n.430G>A		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.465

AC:

70540

AN:

151838

Hom.:

17275

Cov.:

show subpopulations

Gnomad AFR

AF:

0.301

Gnomad AMI

AF:

0.447

Gnomad AMR

AF:

0.565

Gnomad ASJ

AF:

0.423

Gnomad EAS

AF:

0.599

Gnomad SAS

AF:

0.506

Gnomad FIN

AF:

0.546

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.519

Gnomad OTH

AF:

0.459

GnomAD2 exomes

AF:

0.523

AC:

131515

AN:

251372

AF XY:

0.522

show subpopulations

Gnomad AFR exome

AF:

0.299

Gnomad AMR exome

AF:

0.629

Gnomad ASJ exome

AF:

0.425

Gnomad EAS exome

AF:

0.613

Gnomad FIN exome

AF:

0.534

Gnomad NFE exome

AF:

0.515

Gnomad OTH exome

AF:

0.515

GnomAD4 exome

AF:

0.522

AC:

762859

AN:

1461730

Hom.:

200846

Cov.:

AF XY:

0.522

AC XY:

379451

AN XY:

727168

show subpopulations

African (AFR)

AF:

0.292

AC:

9784

AN:

33474

American (AMR)

AF:

0.618

AC:

27624

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.430

AC:

11226

AN:

26130

East Asian (EAS)

AF:

0.601

AC:

23844

AN:

39688

South Asian (SAS)

AF:

0.522

AC:

45048

AN:

86254

European-Finnish (FIN)

AF:

0.531

AC:

28344

AN:

53406

Middle Eastern (MID)

AF:

0.437

AC:

2522

AN:

5768

European-Non Finnish (NFE)

AF:

0.525

AC:

583704

AN:

1111898

Other (OTH)

AF:

0.509

AC:

30763

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

20510

41020

61529

82039

102549

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16752

33504

50256

67008

83760

<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:

0.464

AC:

70568

AN:

151956

Hom.:

17286

Cov.:

AF XY:

0.470

AC XY:

34928

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.300

AC:

12443

AN:

41436

American (AMR)

AF:

0.566

AC:

8634

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.423

AC:

1465

AN:

3462

East Asian (EAS)

AF:

0.598

AC:

3085

AN:

5156

South Asian (SAS)

AF:

0.506

AC:

2441

AN:

4820

European-Finnish (FIN)

AF:

0.546

AC:

5775

AN:

10568

Middle Eastern (MID)

AF:

0.381

AC:

112

AN:

294

European-Non Finnish (NFE)

AF:

0.519

AC:

35255

AN:

67946

Other (OTH)

AF:

0.453

AC:

952

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1877

3755

5632

7510

9387

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

652

1304

1956

2608

3260

<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:

0.497

Hom.:

78907

Bravo

AF:

0.458

Asia WGS

AF:

0.484

AC:

1686

AN:

3478

EpiCase

AF:

0.509

EpiControl

AF:

0.503

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

7.7

(source)

DANN

Benign

0.82

PhyloP100

0.21

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

Mutation Taster

=92/8

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