Variant 3-186582116-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_016306.6(DNAJB11):c.682+39T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 1,500,536 control chromosomes in the GnomAD database, including 31,999 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 6859 hom., cov: 32)

Exomes 𝑓: 0.18 ( 25140 hom. )

Consequence

DNAJB11
NM_016306.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.918

Variant links:

Genes affected

DNAJB11 (HGNC:14889): (DnaJ heat shock protein family (Hsp40) member B11) This gene encodes a soluble glycoprotein of the endoplasmic reticulum (ER) lumen that functions as a co-chaperone of binding immunoglobulin protein, a 70 kilodalton heat shock protein chaperone required for the proper folding and assembly of proteins in the ER. The encoded protein contains a highly conserved J domain of about 70 amino acids with a characteristic His-Pro-Asp (HPD) motif and may regulate the activity of binding immunoglobulin protein by stimulating ATPase activity. [provided by RefSeq, Mar 2014]

DNAJB11 links:

ENSG00000283149 (HGNC:):

ENSG00000283149 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 3-186582116-T-C is Benign according to our data. Variant chr3-186582116-T-C is described in ClinVar as [Benign]. Clinvar id is 1228752.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJB11	NM_016306.6 linkuse as main transcript	c.682+39T>C		intron_variant		ENST00000265028.8	NP_057390.1	Q9UBS4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJB11	ENST00000265028.8 linkuse as main transcript	c.682+39T>C		intron_variant		1	NM_016306.6	ENSP00000265028.3		Q9UBS4
ENSG00000283149	ENST00000418776.1 linkuse as main transcript	c.82+39T>C		intron_variant		3		ENSP00000408410.1		H7C2Y5

Frequencies

GnomAD3 genomes

AF:

0.267

AC:

40531

AN:

151770

Hom.:

6838

Cov.:

show subpopulations

Gnomad AFR

AF:

0.478

Gnomad AMI

AF:

0.0736

Gnomad AMR

AF:

0.237

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.148

Gnomad SAS

AF:

0.250

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.169

Gnomad OTH

AF:

0.274

GnomAD3 exomes

AF:

0.218

AC:

51463

AN:

235888

Hom.:

6294

AF XY:

0.213

AC XY:

27171

AN XY:

127272

show subpopulations

Gnomad AFR exome

AF:

0.493

Gnomad AMR exome

AF:

0.233

Gnomad ASJ exome

AF:

0.222

Gnomad EAS exome

AF:

0.144

Gnomad SAS exome

AF:

0.259

Gnomad FIN exome

AF:

0.212

Gnomad NFE exome

AF:

0.176

Gnomad OTH exome

AF:

0.202

GnomAD4 exome

AF:

0.184

AC:

248022

AN:

1348648

Hom.:

25140

Cov.:

AF XY:

0.185

AC XY:

125058

AN XY:

676138

show subpopulations

Gnomad4 AFR exome

AF:

0.489

Gnomad4 AMR exome

AF:

0.235

Gnomad4 ASJ exome

AF:

0.218

Gnomad4 EAS exome

AF:

0.164

Gnomad4 SAS exome

AF:

0.253

Gnomad4 FIN exome

AF:

0.204

Gnomad4 NFE exome

AF:

0.164

Gnomad4 OTH exome

AF:

0.202

GnomAD4 genome

AF:

0.267

AC:

40589

AN:

151888

Hom.:

6859

Cov.:

AF XY:

0.268

AC XY:

19875

AN XY:

74220

show subpopulations

Gnomad4 AFR

AF:

0.478

Gnomad4 AMR

AF:

0.237

Gnomad4 ASJ

AF:

0.224

Gnomad4 EAS

AF:

0.147

Gnomad4 SAS

AF:

0.250

Gnomad4 FIN

AF:

0.214

Gnomad4 NFE

AF:

0.169

Gnomad4 OTH

AF:

0.273

Alfa

AF:

0.226

Hom.:

1073

Bravo

AF:

0.276

Asia WGS

AF:

0.215

AC:

748

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 11, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.1

DANN

Benign

0.46

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over