Variant 3-132447422-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_015268.4(DNAJC13):c.246T>G(p.Thr82=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 1,608,608 control chromosomes in the GnomAD database, including 13,436 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 1021 hom., cov: 32)

Exomes 𝑓: 0.13 ( 12415 hom. )

Consequence

DNAJC13
NM_015268.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -1.54

Variant links:

Genes affected

DNAJC13 (HGNC:30343): (DnaJ heat shock protein family (Hsp40) member C13) This gene encodes a member of the Dnaj protein family whose members act as co-chaperones of a partner heat-shock protein by binding to the latter and stimulating ATP hydrolysis. The encoded protein associates with the heat-shock protein Hsc70 and plays a role in clathrin-mediated endocytosis. It may also be involved in post-endocytic transport mechanisms via its associations with other proteins, including the sorting nexin SNX1. Mutations in this gene are associated with Parkinson's disease. [provided by RefSeq, Jun 2016]

DNAJC13 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 3-132447422-T-G is Benign according to our data. Variant chr3-132447422-T-G is described in ClinVar as [Benign]. Clinvar id is 1210107.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-132447422-T-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-1.54 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
DNAJC13	NM_015268.4 linkuse as main transcript	c.246T>G	p.Thr82=	synonymous_variant	4/56	ENST00000260818.11	NP_056083.3
DNAJC13	NM_001329126.2 linkuse as main transcript	c.246T>G	p.Thr82=	synonymous_variant	4/57		NP_001316055.1
DNAJC13	XM_047447819.1 linkuse as main transcript	c.246T>G	p.Thr82=	synonymous_variant	4/57		XP_047303775.1
DNAJC13	XM_047447820.1 linkuse as main transcript	c.246T>G	p.Thr82=	synonymous_variant	4/56		XP_047303776.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
DNAJC13	ENST00000260818.11 linkuse as main transcript	c.246T>G	p.Thr82=	synonymous_variant	4/56	1	NM_015268.4	ENSP00000260818	P1
DNAJC13	ENST00000486798.5 linkuse as main transcript	n.311T>G		non_coding_transcript_exon_variant	4/20	1
DNAJC13	ENST00000650455.1 linkuse as main transcript	c.246T>G	p.Thr82=	synonymous_variant, NMD_transcript_variant	4/57			ENSP00000496825

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15764

AN:

151970

Hom.:

1021

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0237

Gnomad AMI

AF:

0.0581

Gnomad AMR

AF:

0.129

Gnomad ASJ

AF:

0.149

Gnomad EAS

AF:

0.128

Gnomad SAS

AF:

0.164

Gnomad FIN

AF:

0.194

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.112

GnomAD3 exomes

AF:

0.133

AC:

32594

AN:

245448

Hom.:

2416

AF XY:

0.136

AC XY:

18065

AN XY:

133010

show subpopulations

Gnomad AFR exome

AF:

0.0218

Gnomad AMR exome

AF:

0.162

Gnomad ASJ exome

AF:

0.145

Gnomad EAS exome

AF:

0.131

Gnomad SAS exome

AF:

0.169

Gnomad FIN exome

AF:

0.180

Gnomad NFE exome

AF:

0.120

Gnomad OTH exome

AF:

0.135

GnomAD4 exome

AF:

0.127

AC:

184766

AN:

1456520

Hom.:

12415

Cov.:

AF XY:

0.129

AC XY:

93237

AN XY:

724568

show subpopulations

Gnomad4 AFR exome

AF:

0.0183

Gnomad4 AMR exome

AF:

0.157

Gnomad4 ASJ exome

AF:

0.144

Gnomad4 EAS exome

AF:

0.146

Gnomad4 SAS exome

AF:

0.170

Gnomad4 FIN exome

AF:

0.177

Gnomad4 NFE exome

AF:

0.122

Gnomad4 OTH exome

AF:

0.123

GnomAD4 genome

AF:

0.104

AC:

15764

AN:

152088

Hom.:

1021

Cov.:

AF XY:

0.109

AC XY:

8113

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.0237

Gnomad4 AMR

AF:

0.129

Gnomad4 ASJ

AF:

0.149

Gnomad4 EAS

AF:

0.128

Gnomad4 SAS

AF:

0.165

Gnomad4 FIN

AF:

0.194

Gnomad4 NFE

AF:

0.125

Gnomad4 OTH

AF:

0.111

Alfa

AF:

0.112

Hom.:

554

Bravo

AF:

0.0946

Asia WGS

AF:

0.135

AC:

471

AN:

3476

EpiCase

AF:

0.131

EpiControl

AF:

0.129

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 05, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

5.9

DANN

Benign

0.63

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

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