Variant rs3962158 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_006145.3(DNAJB1):c.12C>T(p.Asp4Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 1,584,304 control chromosomes in the GnomAD database, including 85,744 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 0.35 ( 9468 hom., cov: 34)

Exomes 𝑓: 0.32 ( 76276 hom. )

Consequence

DNAJB1
NM_006145.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.168

Variant links:

Genes affected

DNAJB1 (HGNC:5270): (DnaJ heat shock protein family (Hsp40) member B1) This gene encodes a member of the DnaJ or Hsp40 (heat shock protein 40 kD) family of proteins. DNAJ family members are characterized by a highly conserved amino acid stretch called the 'J-domain' and function as one of the two major classes of molecular chaperones involved in a wide range of cellular events, such as protein folding and oligomeric protein complex assembly. The encoded protein is a molecular chaperone that stimulates the ATPase activity of Hsp70 heat-shock proteins in order to promote protein folding and prevent misfolded protein aggregation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]

DNAJB1 links:

TECR (HGNC:):

TECR links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP7

Synonymous conserved (PhyloP=0.168 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJB1	NM_006145.3 linkuse as main transcript	c.12C>T	p.Asp4Asp	synonymous_variant	1/3	ENST00000254322.3	NP_006136.1	P25685-1Q6FHS4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJB1	ENST00000254322.3 linkuse as main transcript	c.12C>T	p.Asp4Asp	synonymous_variant	1/3	1	NM_006145.3	ENSP00000254322.1		P25685-1

Frequencies

GnomAD3 genomes

AF:

0.345

AC:

52404

AN:

151942

Hom.:

9442

Cov.:

show subpopulations

Gnomad AFR

AF:

0.419

Gnomad AMI

AF:

0.475

Gnomad AMR

AF:

0.332

Gnomad ASJ

AF:

0.330

Gnomad EAS

AF:

0.0920

Gnomad SAS

AF:

0.433

Gnomad FIN

AF:

0.387

Gnomad MID

AF:

0.394

Gnomad NFE

AF:

0.309

Gnomad OTH

AF:

0.323

GnomAD3 exomes

AF:

0.341

AC:

74785

AN:

219030

Hom.:

13357

AF XY:

0.342

AC XY:

41324

AN XY:

120710

show subpopulations

Gnomad AFR exome

AF:

0.420

Gnomad AMR exome

AF:

0.401

Gnomad ASJ exome

AF:

0.352

Gnomad EAS exome

AF:

0.0908

Gnomad SAS exome

AF:

0.440

Gnomad FIN exome

AF:

0.399

Gnomad NFE exome

AF:

0.316

Gnomad OTH exome

AF:

0.334

GnomAD4 exome

AF:

0.321

AC:

460227

AN:

1432244

Hom.:

76276

Cov.:

AF XY:

0.324

AC XY:

231003

AN XY:

712738

show subpopulations

Gnomad4 AFR exome

AF:

0.423

Gnomad4 AMR exome

AF:

0.393

Gnomad4 ASJ exome

AF:

0.341

Gnomad4 EAS exome

AF:

0.0845

Gnomad4 SAS exome

AF:

0.427

Gnomad4 FIN exome

AF:

0.392

Gnomad4 NFE exome

AF:

0.313

Gnomad4 OTH exome

AF:

0.321

GnomAD4 genome

AF:

0.345

AC:

52475

AN:

152060

Hom.:

9468

Cov.:

AF XY:

0.348

AC XY:

25900

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.419

Gnomad4 AMR

AF:

0.332

Gnomad4 ASJ

AF:

0.330

Gnomad4 EAS

AF:

0.0924

Gnomad4 SAS

AF:

0.433

Gnomad4 FIN

AF:

0.387

Gnomad4 NFE

AF:

0.309

Gnomad4 OTH

AF:

0.320

Alfa

AF:

0.325

Hom.:

1727

Bravo

AF:

0.342

Asia WGS

AF:

0.273

AC:

948

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

7.7

DANN

Benign

0.96

RBP_binding_hub_radar

1.0

RBP_regulation_power_radar

2.7

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over