NM_153614.4:c.882C>T

Variant names:

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_153614.4(DNAJB13):c.882C>T(p.Phe294Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 1,609,274 control chromosomes in the GnomAD database, including 68,644 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 6202 hom., cov: 32)

Exomes 𝑓: 0.29 ( 62442 hom. )

Consequence

DNAJB13
NM_153614.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.10

Publications

21 publications found

Variant links:

Genes affected

DNAJB13 (HGNC:30718): (DnaJ heat shock protein family (Hsp40) member B13) This gene encodes a member of the heat shock protein 40 co-chaperone family which is produced in large amounts in the testis and is located on the radial spokes of the axoneme in human sperm flagella and other flagellar structures. The encoded protein associates with the sperm annulus, as part of the septin complex, through direct interaction with septin 4, during sperm terminal differentiation. Naturally occurring mutations in this gene are associated with primary ciliary dyskinesia and male infertility. [provided by RefSeq, Apr 2017]

DNAJB13 Gene-Disease associations (from GenCC):

primary ciliary dyskinesia 34
Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, PanelApp Australia, G2P, Labcorp Genetics (formerly Invitae)
primary ciliary dyskinesia
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

DNAJB13 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 11-73970045-C-T is Benign according to our data. Variant chr11-73970045-C-T is described in ClinVar as [Benign]. Clinvar id is 1253105.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.1 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJB13	NM_153614.4 link	c.882C>T	p.Phe294Phe	synonymous_variant	Exon 8 of 8	ENST00000339764.6	NP_705842.2	P59910-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
DNAJB13	ENST00000339764.6 link	c.882C>T	p.Phe294Phe	synonymous_variant	Exon 8 of 8	1	NM_153614.4	ENSP00000344431.1	P59910-1
DNAJB13	ENST00000543947.1 link	c.357C>T	p.Phe119Phe	synonymous_variant	Exon 5 of 6	1		ENSP00000438576.1	P59910-2
DNAJB13	ENST00000542350.5 link	c.582C>T	p.Phe194Phe	synonymous_variant	Exon 5 of 5	3		ENSP00000440778.1	H0YFX2
DNAJB13	ENST00000537753.5 link	c.357C>T	p.Phe119Phe	synonymous_variant	Exon 5 of 5	3		ENSP00000439711.1	P59910-2

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42433

AN:

151876

Hom.:

6205

Cov.:

show subpopulations

Gnomad AFR

AF:

0.219

Gnomad AMI

AF:

0.374

Gnomad AMR

AF:

0.358

Gnomad ASJ

AF:

0.294

Gnomad EAS

AF:

0.151

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.310

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.305

Gnomad OTH

AF:

0.309

GnomAD2 exomes

AF:

0.285

AC:

69953

AN:

245486

AF XY:

0.282

show subpopulations

Gnomad AFR exome

AF:

0.218

Gnomad AMR exome

AF:

0.367

Gnomad ASJ exome

AF:

0.292

Gnomad EAS exome

AF:

0.129

Gnomad FIN exome

AF:

0.303

Gnomad NFE exome

AF:

0.307

Gnomad OTH exome

AF:

0.304

GnomAD4 exome

AF:

0.290

AC:

422136

AN:

1457280

Hom.:

62442

Cov.:

AF XY:

0.288

AC XY:

208524

AN XY:

724702

show subpopulations

African (AFR)

AF:

0.214

AC:

7150

AN:

33396

American (AMR)

AF:

0.370

AC:

16273

AN:

44030

Ashkenazi Jewish (ASJ)

AF:

0.296

AC:

7697

AN:

26036

East Asian (EAS)

AF:

0.177

AC:

7002

AN:

39566

South Asian (SAS)

AF:

0.228

AC:

19395

AN:

85142

European-Finnish (FIN)

AF:

0.305

AC:

16251

AN:

53360

Middle Eastern (MID)

AF:

0.328

AC:

1883

AN:

5746

European-Non Finnish (NFE)

AF:

0.297

AC:

329638

AN:

1109766

Other (OTH)

AF:

0.280

AC:

16847

AN:

60238

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

17107

34214

51322

68429

85536

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10748

21496

32244

42992

53740

<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:

0.279

AC:

42443

AN:

151994

Hom.:

6202

Cov.:

AF XY:

0.279

AC XY:

20689

AN XY:

74278

show subpopulations

African (AFR)

AF:

0.218

AC:

9055

AN:

41466

American (AMR)

AF:

0.359

AC:

5472

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.294

AC:

1018

AN:

3466

East Asian (EAS)

AF:

0.151

AC:

781

AN:

5176

South Asian (SAS)

AF:

0.215

AC:

1037

AN:

4814

European-Finnish (FIN)

AF:

0.310

AC:

3267

AN:

10546

Middle Eastern (MID)

AF:

0.350

AC:

103

AN:

294

European-Non Finnish (NFE)

AF:

0.305

AC:

20727

AN:

67958

Other (OTH)

AF:

0.305

AC:

642

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1569

3138

4707

6276

7845

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

424

848

1272

1696

2120

<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:

0.300

Hom.:

11665

Bravo

AF:

0.283

Asia WGS

AF:

0.191

AC:

664

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Nov 10, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

4.3

(source)

DANN

Benign

0.84

PhyloP100

-1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over