Variant chr3-186571021-G-A 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.68+56G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 1,003,232 control chromosomes in the GnomAD database, including 11,931 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 4436 hom., cov: 28)

Exomes 𝑓: 0.092 ( 7495 hom. )

Consequence

DNAJB11
NM_016306.6 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.50

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:

DNAJB11 (HGNC:):

DNAJB11 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 3-186571021-G-A is Benign according to our data. Variant chr3-186571021-G-A is described in ClinVar as [Benign]. Clinvar id is 1283656.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 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.68+56G>A		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.68+56G>A		intron_variant		1	NM_016306.6	ENSP00000265028.3		Q9UBS4

Frequencies

GnomAD3 genomes

AF:

0.215

AC:

32349

AN:

150378

Hom.:

4425

Cov.:

show subpopulations

Gnomad AFR

AF:

0.390

Gnomad AMI

AF:

0.0747

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.183

Gnomad EAS

AF:

0.141

Gnomad SAS

AF:

0.235

Gnomad FIN

AF:

0.175

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.128

Gnomad OTH

AF:

0.212

GnomAD4 exome

AF:

0.0924

AC:

78796

AN:

852738

Hom.:

7495

AF XY:

0.0980

AC XY:

42382

AN XY:

432548

show subpopulations

Gnomad4 AFR exome

AF:

0.303

Gnomad4 AMR exome

AF:

0.147

Gnomad4 ASJ exome

AF:

0.151

Gnomad4 EAS exome

AF:

0.141

Gnomad4 SAS exome

AF:

0.207

Gnomad4 FIN exome

AF:

0.166

Gnomad4 NFE exome

AF:

0.0635

Gnomad4 OTH exome

AF:

0.118

GnomAD4 genome

AF:

0.215

AC:

32390

AN:

150494

Hom.:

4436

Cov.:

AF XY:

0.217

AC XY:

15951

AN XY:

73460

show subpopulations

Gnomad4 AFR

AF:

0.390

Gnomad4 AMR

AF:

0.197

Gnomad4 ASJ

AF:

0.183

Gnomad4 EAS

AF:

0.141

Gnomad4 SAS

AF:

0.235

Gnomad4 FIN

AF:

0.175

Gnomad4 NFE

AF:

0.128

Gnomad4 OTH

AF:

0.212

Alfa

AF:

0.194

Hom.:

411

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

8.4

DANN

Benign

0.94

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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