Genetic Variant DNAJC11:c.1098-16_1098-15dupTT (chr1-6640071-C-CAA) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_018198.4(DNAJC11):c.1098-16_1098-15dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0019 ( 2 hom., cov: 0)

Exomes 𝑓: 0.012 ( 3 hom. )

Consequence

DNAJC11
NM_018198.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.23

Publications

0 publications found

Variant links:

Genes affected

DNAJC11 (HGNC:25570): (DnaJ heat shock protein family (Hsp40) member C11) Involved in cristae formation. Located in mitochondrial outer membrane and nuclear speck. Part of MIB complex. Colocalizes with MICOS complex and SAM complex. [provided by Alliance of Genome Resources, Apr 2022]

DNAJC11 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 2 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018198.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJC11	NM_018198.4	MANE Select	c.1098-16_1098-15dupTT		intron	N/A	NP_060668.2	Q9NVH1-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DNAJC11	ENST00000377577.10	TSL:1 MANE Select	c.1098-15_1098-14insTT	intron	N/A	ENSP00000366800.5	Q9NVH1-1
DNAJC11	ENST00000294401.11	TSL:1	c.1098-1708_1098-1707insTT	intron	N/A	ENSP00000294401.7	Q9NVH1-3
DNAJC11	ENST00000451196.5	TSL:1	c.741-5288_741-5287insTT	intron	N/A	ENSP00000415871.1	Q5TH61

Frequencies

GnomAD3 genomes

AF:

0.00188

AC:

155

AN:

82494

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00125

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00412

Gnomad ASJ

AF:

0.000419

Gnomad EAS

AF:

0.00338

Gnomad SAS

AF:

0.00647

Gnomad FIN

AF:

0.000954

Gnomad MID

AF:

0.00538

Gnomad NFE

AF:

0.00153

Gnomad OTH

AF:

0.000894

GnomAD2 exomes

AF:

0.0331

AC:

874

AN:

26422

AF XY:

0.0342

show subpopulations

Gnomad AFR exome

AF:

0.0286

Gnomad AMR exome

AF:

0.0316

Gnomad ASJ exome

AF:

0.0404

Gnomad EAS exome

AF:

0.0376

Gnomad FIN exome

AF:

0.0102

Gnomad NFE exome

AF:

0.0291

Gnomad OTH exome

AF:

0.0379

GnomAD4 exome

AF:

0.0124

AC:

14013

AN:

1127456

Hom.:

Cov.:

AF XY:

0.0131

AC XY:

7132

AN XY:

544216

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.0114

AC:

274

AN:

24008

American (AMR)

AF:

0.0198

AC:

302

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0179

AC:

273

AN:

15210

East Asian (EAS)

AF:

0.0215

AC:

585

AN:

27178

South Asian (SAS)

AF:

0.0314

AC:

1563

AN:

49698

European-Finnish (FIN)

AF:

0.0162

AC:

395

AN:

24364

Middle Eastern (MID)

AF:

0.0189

AC:

AN:

3020

European-Non Finnish (NFE)

AF:

0.0108

AC:

9946

AN:

923256

Other (OTH)

AF:

0.0136

AC:

618

AN:

45438

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.319

Heterozygous variant carriers

897

1794

2692

3589

4486

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

340

680

1020

1360

1700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00188

AC:

155

AN:

82466

Hom.:

Cov.:

AF XY:

0.00219

AC XY:

AN XY:

38376

show subpopulations

African (AFR)

AF:

0.00125

AC:

AN:

20008

American (AMR)

AF:

0.00412

AC:

AN:

7286

Ashkenazi Jewish (ASJ)

AF:

0.000419

AC:

AN:

2384

East Asian (EAS)

AF:

0.00340

AC:

AN:

3234

South Asian (SAS)

AF:

0.00651

AC:

AN:

2918

European-Finnish (FIN)

AF:

0.000954

AC:

AN:

3146

Middle Eastern (MID)

AF:

0.00610

AC:

AN:

164

European-Non Finnish (NFE)

AF:

0.00153

AC:

AN:

41782

Other (OTH)

AF:

0.000885

AC:

AN:

1130

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.2

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

1-6640071-CAAAAAA-CAAAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over