chr3-186571884-T-G

Position:

• chr3-186571884-T-G

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.69-211T>G 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 152,160 control chromosomes in the GnomAD database, including 6,778 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.27 (6778 hom., cov: 33)
• Consequence: DNAJB11 NM_016306.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.14

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=-0.85).
• BP6: Variant 3-186571884-T-G is Benign according to our data. Variant chr3-186571884-T-G is described in ClinVar as [Benign]. Clinvar id is 1275544.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJB11	NM_016306.6	c.69-211T>G		intron_variant		ENST00000265028.8	NP_057390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJB11	ENST00000265028.8	c.69-211T>G		intron_variant		1	NM_016306.6	ENSP00000265028.3

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40400 AN: 152042 Hom.: 6757 Cov.: 33

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.291

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: 40458 AN: 152160 Hom.: 6778 Cov.: 33 AF XY: 0.266 AC XY: 19816 AN XY: 74392

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.270

Alfa AF: 0.233 Hom.: 882

Bravo AF: 0.275

Asia WGS AF: 0.209 AC: 727 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	-0.85
CADD	Benign	6.9
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

Other links and lift over

dbSNP: rs713484; hg19: chr3-186289673;