Variant rs2306819 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_153614.4(DNAJB13):c.882C>T(p.Phe294=) 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

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	UniProt
DNAJB13	NM_153614.4 linkuse as main transcript	c.882C>T	p.Phe294=	synonymous_variant	8/8	ENST00000339764.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAJB13	ENST00000339764.6 linkuse as main transcript	c.882C>T	p.Phe294=	synonymous_variant	8/8	1	NM_153614.4	P1	P59910-1
DNAJB13	ENST00000543947.1 linkuse as main transcript	c.357C>T	p.Phe119=	synonymous_variant	5/6	1			P59910-2
DNAJB13	ENST00000542350.5 linkuse as main transcript	c.585C>T	p.Phe195=	synonymous_variant	5/5	3
DNAJB13	ENST00000537753.5 linkuse as main transcript	c.357C>T	p.Phe119=	synonymous_variant	5/5	3			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

GnomAD3 exomes

AF:

0.285

AC:

69953

AN:

245486

Hom.:

10677

AF XY:

0.282

AC XY:

37434

AN XY:

132906

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 SAS exome

AF:

0.224

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

Gnomad4 AFR exome

AF:

0.214

Gnomad4 AMR exome

AF:

0.370

Gnomad4 ASJ exome

AF:

0.296

Gnomad4 EAS exome

AF:

0.177

Gnomad4 SAS exome

AF:

0.228

Gnomad4 FIN exome

AF:

0.305

Gnomad4 NFE exome

AF:

0.297

Gnomad4 OTH exome

AF:

0.280

GnomAD4 genome

AF:

0.279

AC:

42443

AN:

151994

Hom.:

6202

Cov.:

AF XY:

0.279

AC XY:

20689

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.218

Gnomad4 AMR

AF:

0.359

Gnomad4 ASJ

AF:

0.294

Gnomad4 EAS

AF:

0.151

Gnomad4 SAS

AF:

0.215

Gnomad4 FIN

AF:

0.310

Gnomad4 NFE

AF:

0.305

Gnomad4 OTH

AF:

0.305

Alfa

AF:

0.302

Hom.:

8716

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

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

4.3

DANN

Benign

0.84

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over