Genetic Variant DNAJC11:c.*404C>A (chr1-6635271-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018198.4(DNAJC11):c.*404C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 182,400 control chromosomes in the GnomAD database, including 9,950 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.33 ( 8398 hom., cov: 33)

Exomes 𝑓: 0.32 ( 1552 hom. )

Consequence

DNAJC11
NM_018198.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.135

Publications

9 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:

THAP3 (HGNC:20855): (THAP domain containing 3) Predicted to enable DNA binding activity and metal ion binding activity. Involved in positive regulation of transcription by RNA polymerase II. [provided by Alliance of Genome Resources, Apr 2022]

THAP3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

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

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJC11	NM_018198.4 link	c.*404C>A		3_prime_UTR_variant	Exon 16 of 16	ENST00000377577.10	NP_060668.2	Q9NVH1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAJC11	ENST00000377577.10 link	c.*404C>A		3_prime_UTR_variant	Exon 16 of 16	1	NM_018198.4	ENSP00000366800.5		Q9NVH1-1

Frequencies

GnomAD3 genomes

AF:

0.327

AC:

49791

AN:

152056

Hom.:

8389

Cov.:

show subpopulations

Gnomad AFR

AF:

0.315

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.303

Gnomad ASJ

AF:

0.390

Gnomad EAS

AF:

0.408

Gnomad SAS

AF:

0.434

Gnomad FIN

AF:

0.266

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.335

Gnomad OTH

AF:

0.348

GnomAD4 exome

AF:

0.316

AC:

9543

AN:

30226

Hom.:

1552

Cov.:

AF XY:

0.327

AC XY:

5147

AN XY:

15734

show subpopulations

African (AFR)

AF:

0.275

AC:

310

AN:

1128

American (AMR)

AF:

0.279

AC:

962

AN:

3450

Ashkenazi Jewish (ASJ)

AF:

0.391

AC:

269

AN:

688

East Asian (EAS)

AF:

0.379

AC:

874

AN:

2304

South Asian (SAS)

AF:

0.393

AC:

1265

AN:

3216

European-Finnish (FIN)

AF:

0.253

AC:

302

AN:

1192

Middle Eastern (MID)

AF:

0.419

AC:

AN:

European-Non Finnish (NFE)

AF:

0.305

AC:

5088

AN:

16686

Other (OTH)

AF:

0.298

AC:

447

AN:

1500

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

302

605

907

1210

1512

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

118

236

354

472

590

<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:

0.327

AC:

49821

AN:

152174

Hom.:

8398

Cov.:

AF XY:

0.327

AC XY:

24353

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.315

AC:

13070

AN:

41516

American (AMR)

AF:

0.303

AC:

4640

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.390

AC:

1354

AN:

3472

East Asian (EAS)

AF:

0.408

AC:

2111

AN:

5168

South Asian (SAS)

AF:

0.435

AC:

2098

AN:

4824

European-Finnish (FIN)

AF:

0.266

AC:

2815

AN:

10596

Middle Eastern (MID)

AF:

0.391

AC:

115

AN:

294

European-Non Finnish (NFE)

AF:

0.335

AC:

22777

AN:

67980

Other (OTH)

AF:

0.348

AC:

735

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1736

3471

5207

6942

8678

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

502

1004

1506

2008

2510

<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:

0.308

Hom.:

3420

Bravo

AF:

0.327

Asia WGS

AF:

0.399

AC:

1387

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.4

(source)

DANN

Benign

0.60

PhyloP100

-0.14

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over