Genetic Variant DNAJC15:c.108+107C>G (chr13-43023841-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_013238.3(DNAJC15):c.108+107C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 1,061,602 control chromosomes in the GnomAD database, including 25,093 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 0.22 ( 3758 hom., cov: 32)

Exomes 𝑓: 0.21 ( 21335 hom. )

Consequence

DNAJC15
NM_013238.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0490

Publications

16 publications found

Variant links:

Genes affected

DNAJC15 (HGNC:20325): (DnaJ heat shock protein family (Hsp40) member C15) Predicted to enable ATPase activator activity. Predicted to be involved in protein import into mitochondrial matrix. Predicted to act upstream of or within several processes, including cellular response to starvation; negative regulation of mitochondrial electron transport, NADH to ubiquinone; and negative regulation of protein-containing complex assembly. Predicted to be located in mitochondrial inner membrane. Predicted to be part of PAM complex, Tim23 associated import motor. [provided by Alliance of Genome Resources, Apr 2022]

DNAJC15 links:

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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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJC15	NM_013238.3 link	c.108+107C>G		intron_variant	Intron 1 of 5	ENST00000379221.4	NP_037370.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAJC15	ENST00000379221.4 link	c.108+107C>G		intron_variant	Intron 1 of 5	1	NM_013238.3	ENSP00000368523.2
DNAJC15	ENST00000474320.1 link	n.532+107C>G		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.222

AC:

33706

AN:

151996

Hom.:

3754

Cov.:

show subpopulations

Gnomad AFR

AF:

0.223

Gnomad AMI

AF:

0.328

Gnomad AMR

AF:

0.185

Gnomad ASJ

AF:

0.219

Gnomad EAS

AF:

0.0895

Gnomad SAS

AF:

0.138

Gnomad FIN

AF:

0.246

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.216

GnomAD4 exome

AF:

0.211

AC:

191949

AN:

909488

Hom.:

21335

AF XY:

0.209

AC XY:

95304

AN XY:

456440

show subpopulations

African (AFR)

AF:

0.210

AC:

4604

AN:

21900

American (AMR)

AF:

0.160

AC:

4557

AN:

28462

Ashkenazi Jewish (ASJ)

AF:

0.208

AC:

3922

AN:

18864

East Asian (EAS)

AF:

0.0803

AC:

2663

AN:

33162

South Asian (SAS)

AF:

0.134

AC:

8330

AN:

62108

European-Finnish (FIN)

AF:

0.233

AC:

7549

AN:

32438

Middle Eastern (MID)

AF:

0.175

AC:

811

AN:

4642

European-Non Finnish (NFE)

AF:

0.227

AC:

151031

AN:

665992

Other (OTH)

AF:

0.202

AC:

8482

AN:

41920

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

7064

14127

21191

28254

35318

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4258

8516

12774

17032

21290

<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:

0.222

AC:

33736

AN:

152114

Hom.:

3758

Cov.:

AF XY:

0.218

AC XY:

16205

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.223

AC:

9239

AN:

41494

American (AMR)

AF:

0.185

AC:

2826

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.219

AC:

762

AN:

3472

East Asian (EAS)

AF:

0.0899

AC:

464

AN:

5162

South Asian (SAS)

AF:

0.139

AC:

672

AN:

4830

European-Finnish (FIN)

AF:

0.246

AC:

2604

AN:

10582

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.240

AC:

16342

AN:

67972

Other (OTH)

AF:

0.217

AC:

458

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1375

2750

4126

5501

6876

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

354

708

1062

1416

1770

<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:

0.142

Hom.:

267

Bravo

AF:

0.218

Asia WGS

AF:

0.138

AC:

481

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.5

(source)

DANN

Benign

0.40

PhyloP100

0.049

PromoterAI

0.056

Neutral

(source)

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

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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