Variant 17-41994952-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003315.4(DNAJC7):c.406-8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 1,610,414 control chromosomes in the GnomAD database, including 565,550 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.75 ( 44640 hom., cov: 33)

Exomes 𝑓: 0.84 ( 520910 hom. )

Consequence

DNAJC7
NM_003315.4 splice_region, intron

Scores

Splicing: ADA: 0.00002760

Clinical Significance

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

Conservation

PhyloP100: -0.773

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

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

BP6

Variant 17-41994952-G-A is Benign according to our data. Variant chr17-41994952-G-A is described in ClinVar as [Benign]. Clinvar id is 1294632.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.846 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.406-8C>T		splice_region_variant, intron_variant		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.406-8C>T		splice_region_variant, intron_variant		1	NM_003315.4	ENSP00000406463.2		Q99615-1

Frequencies

GnomAD3 genomes

AF:

0.749

AC:

113854

AN:

152012

Hom.:

44636

Cov.:

show subpopulations

Gnomad AFR

AF:

0.489

Gnomad AMI

AF:

0.877

Gnomad AMR

AF:

0.857

Gnomad ASJ

AF:

0.871

Gnomad EAS

AF:

0.861

Gnomad SAS

AF:

0.843

Gnomad FIN

AF:

0.795

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.852

Gnomad OTH

AF:

0.779

GnomAD3 exomes

AF:

0.832

AC:

205769

AN:

247392

Hom.:

86700

AF XY:

0.835

AC XY:

112044

AN XY:

134262

show subpopulations

Gnomad AFR exome

AF:

0.487

Gnomad AMR exome

AF:

0.900

Gnomad ASJ exome

AF:

0.867

Gnomad EAS exome

AF:

0.860

Gnomad SAS exome

AF:

0.842

Gnomad FIN exome

AF:

0.802

Gnomad NFE exome

AF:

0.853

Gnomad OTH exome

AF:

0.847

GnomAD4 exome

AF:

0.843

AC:

1229024

AN:

1458284

Hom.:

520910

Cov.:

AF XY:

0.844

AC XY:

612123

AN XY:

725440

show subpopulations

Gnomad4 AFR exome

AF:

0.465

Gnomad4 AMR exome

AF:

0.894

Gnomad4 ASJ exome

AF:

0.867

Gnomad4 EAS exome

AF:

0.864

Gnomad4 SAS exome

AF:

0.846

Gnomad4 FIN exome

AF:

0.810

Gnomad4 NFE exome

AF:

0.853

Gnomad4 OTH exome

AF:

0.829

GnomAD4 genome

AF:

0.749

AC:

113876

AN:

152130

Hom.:

44640

Cov.:

AF XY:

0.750

AC XY:

55795

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.488

Gnomad4 AMR

AF:

0.858

Gnomad4 ASJ

AF:

0.871

Gnomad4 EAS

AF:

0.861

Gnomad4 SAS

AF:

0.844

Gnomad4 FIN

AF:

0.795

Gnomad4 NFE

AF:

0.852

Gnomad4 OTH

AF:

0.773

Alfa

AF:

0.790

Hom.:

22591

Bravo

AF:

0.742

Asia WGS

AF:

0.791

AC:

2750

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	clinical testing	GeneDx	May 04, 2021	- -
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

-0.54

CADD

Benign

0.093

DANN

Benign

0.54

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000028

dbscSNV1_RF

Benign

0.0

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