Genetic Variant NM_018163.3:c.792+35G>A (chr15-40773692-C-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_018163.3(DNAJC17):c.792+35G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 1,564,784 control chromosomes in the GnomAD database, including 87,331 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 0.25 ( 6288 hom., cov: 32)

Exomes 𝑓: 0.33 ( 81043 hom. )

Consequence

DNAJC17
NM_018163.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.229

Publications

19 publications found

Variant links:

Genes affected

DNAJC17 (HGNC:25556): (DnaJ heat shock protein family (Hsp40) member C17) Predicted to enable RNA binding activity. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II and toxin transport. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

DNAJC17 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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJC17	NM_018163.3 link	c.792+35G>A		intron_variant	Intron 10 of 10	ENST00000220496.9	NP_060633.1	Q9NVM6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
DNAJC17	ENST00000220496.9 link	c.792+35G>A	intron_variant	Intron 10 of 10	1	NM_018163.3	ENSP00000220496.4	Q9NVM6
DNAJC17	ENST00000559238.5 link	n.*820+35G>A	intron_variant	Intron 11 of 11	5		ENSP00000453354.1	H0YLV4
DNAJC17	ENST00000561110.5 link	n.339+35G>A	intron_variant	Intron 4 of 4	3
DNAJC17	ENST00000560645.5 link	n.*534G>A	downstream_gene_variant		1		ENSP00000452716.1	H0YK99

Frequencies

GnomAD3 genomes

AF:

0.252

AC:

38387

AN:

152052

Hom.:

6286

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0644

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.208

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.0732

Gnomad SAS

AF:

0.341

Gnomad FIN

AF:

0.435

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.351

Gnomad OTH

AF:

0.244

GnomAD2 exomes

AF:

0.290

AC:

66282

AN:

228200

AF XY:

0.306

show subpopulations

Gnomad AFR exome

AF:

0.0566

Gnomad AMR exome

AF:

0.143

Gnomad ASJ exome

AF:

0.366

Gnomad EAS exome

AF:

0.0698

Gnomad FIN exome

AF:

0.437

Gnomad NFE exome

AF:

0.352

Gnomad OTH exome

AF:

0.321

GnomAD4 exome

AF:

0.330

AC:

465497

AN:

1412612

Hom.:

81043

Cov.:

AF XY:

0.333

AC XY:

233995

AN XY:

703692

show subpopulations

African (AFR)

AF:

0.0538

AC:

1726

AN:

32104

American (AMR)

AF:

0.152

AC:

6363

AN:

41920

Ashkenazi Jewish (ASJ)

AF:

0.362

AC:

8995

AN:

24820

East Asian (EAS)

AF:

0.0833

AC:

3241

AN:

38918

South Asian (SAS)

AF:

0.367

AC:

30424

AN:

82900

European-Finnish (FIN)

AF:

0.436

AC:

22737

AN:

52188

Middle Eastern (MID)

AF:

0.302

AC:

1696

AN:

5620

European-Non Finnish (NFE)

AF:

0.346

AC:

371973

AN:

1075642

Other (OTH)

AF:

0.314

AC:

18342

AN:

58500

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

14584

29168

43751

58335

72919

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11566

23132

34698

46264

57830

<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:

0.252

AC:

38391

AN:

152172

Hom.:

6288

Cov.:

AF XY:

0.256

AC XY:

19061

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.0642

AC:

2668

AN:

41544

American (AMR)

AF:

0.207

AC:

3168

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.358

AC:

1243

AN:

3468

East Asian (EAS)

AF:

0.0731

AC:

379

AN:

5182

South Asian (SAS)

AF:

0.341

AC:

1648

AN:

4826

European-Finnish (FIN)

AF:

0.435

AC:

4604

AN:

10576

Middle Eastern (MID)

AF:

0.354

AC:

104

AN:

294

European-Non Finnish (NFE)

AF:

0.351

AC:

23851

AN:

67968

Other (OTH)

AF:

0.248

AC:

525

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1340

2679

4019

5358

6698

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

394

788

1182

1576

1970

<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:

0.310

Hom.:

9739

Bravo

AF:

0.221

Asia WGS

AF:

0.236

AC:

820

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

5.4

(source)

DANN

Benign

0.62

PhyloP100

-0.23

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