Variant 17-41990284-T-C 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_003315.4(DNAJC7):c.579A>G(p.Pro193Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0761 in 1,609,772 control chromosomes in the GnomAD database, including 5,728 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1120 hom., cov: 32)

Exomes 𝑓: 0.073 ( 4608 hom. )

Consequence

DNAJC7
NM_003315.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.283

Variant links:

Genes affected

DNAJC7 (HGNC:12392): (DnaJ heat shock protein family (Hsp40) member C7) This gene encodes a member of the DNAJ heat shock protein 40 family of proteins that is characterized by two N-terminal tetratricopeptide repeat domains and a C-terminal DNAJ domain. This protein binds the chaperone proteins heat shock proteins 70 and 90 in an ATP-dependent manner and may function as a co-chaperone. Pseudogenes of this gene are found on chromosomes 1 and 6. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Oct 2009]

DNAJC7 links:

DNAJC7 (HGNC:):

DNAJC7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 17-41990284-T-C is Benign according to our data. Variant chr17-41990284-T-C is described in ClinVar as [Benign]. Clinvar id is 1261815.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.283 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJC7	NM_003315.4 linkuse as main transcript	c.579A>G	p.Pro193Pro	synonymous_variant	6/14	ENST00000457167.9	NP_003306.3	Q99615-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJC7	ENST00000457167.9 linkuse as main transcript	c.579A>G	p.Pro193Pro	synonymous_variant	6/14	1	NM_003315.4	ENSP00000406463.2		Q99615-1

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16315

AN:

152090

Hom.:

1106

Cov.:

show subpopulations

Gnomad AFR

AF:

0.199

Gnomad AMI

AF:

0.0548

Gnomad AMR

AF:

0.0586

Gnomad ASJ

AF:

0.0695

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.122

Gnomad FIN

AF:

0.0765

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0667

Gnomad OTH

AF:

0.100

GnomAD3 exomes

AF:

0.0837

AC:

20331

AN:

242778

Hom.:

1063

AF XY:

0.0847

AC XY:

11130

AN XY:

131404

show subpopulations

Gnomad AFR exome

AF:

0.196

Gnomad AMR exome

AF:

0.0412

Gnomad ASJ exome

AF:

0.0731

Gnomad EAS exome

AF:

0.139

Gnomad SAS exome

AF:

0.119

Gnomad FIN exome

AF:

0.0792

Gnomad NFE exome

AF:

0.0662

Gnomad OTH exome

AF:

0.0729

GnomAD4 exome

AF:

0.0728

AC:

106104

AN:

1457564

Hom.:

4608

Cov.:

AF XY:

0.0738

AC XY:

53450

AN XY:

724454

show subpopulations

Gnomad4 AFR exome

AF:

0.205

Gnomad4 AMR exome

AF:

0.0435

Gnomad4 ASJ exome

AF:

0.0738

Gnomad4 EAS exome

AF:

0.136

Gnomad4 SAS exome

AF:

0.114

Gnomad4 FIN exome

AF:

0.0761

Gnomad4 NFE exome

AF:

0.0640

Gnomad4 OTH exome

AF:

0.0800

GnomAD4 genome

AF:

0.108

AC:

16376

AN:

152208

Hom.:

1120

Cov.:

AF XY:

0.108

AC XY:

8057

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.200

Gnomad4 AMR

AF:

0.0584

Gnomad4 ASJ

AF:

0.0695

Gnomad4 EAS

AF:

0.139

Gnomad4 SAS

AF:

0.121

Gnomad4 FIN

AF:

0.0765

Gnomad4 NFE

AF:

0.0667

Gnomad4 OTH

AF:

0.104

Alfa

AF:

0.0812

Hom.:

320

Bravo

AF:

0.108

Asia WGS

AF:

0.143

AC:

497

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

9.7

DANN

Benign

0.69

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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