chr3-186581825-G-A

Position:

• chr3-186581825-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_016306.6(DNAJB11):​c.600-170G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,816 control chromosomes in the GnomAD database, including 6,745 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.27 (6745 hom., cov: 32)
• Consequence: DNAJB11 NM_016306.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0120

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 3-186581825-G-A is Benign according to our data. Variant chr3-186581825-G-A is described in ClinVar as [Benign]. Clinvar id is 1286720.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJB11	NM_016306.6	c.600-170G>A		intron_variant		ENST00000265028.8	NP_057390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJB11	ENST00000265028.8	c.600-170G>A		intron_variant		1	NM_016306.6	ENSP00000265028.3

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40309 AN: 151696 Hom.: 6724 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.271

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.266 AC: 40366 AN: 151816 Hom.: 6745 Cov.: 32 AF XY: 0.267 AC XY: 19782 AN XY: 74184

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.270

Alfa AF: 0.0976 Hom.: 157

Bravo AF: 0.274

Asia WGS AF: 0.214 AC: 743 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

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	4.0
DANN	Benign	0.45

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

Other links and lift over

dbSNP: rs6770868; hg19: chr3-186299614;