Variant rs142025971 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001130183.2(DNAJA4):c.1_2delAT(p.Met1fs) variant causes a frameshift, start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0369 in 1,613,698 control chromosomes in the GnomAD database, including 1,349 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.030 ( 92 hom., cov: 33)

Exomes 𝑓: 0.038 ( 1257 hom. )

Consequence

DNAJA4
NM_001130183.2 frameshift, start_lost

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.141

Variant links:

Genes affected

DNAJA4 (HGNC:14885): (DnaJ heat shock protein family (Hsp40) member A4) Enables chaperone binding activity and unfolded protein binding activity. Involved in several processes, including negative regulation of endothelial cell migration; negative regulation of inclusion body assembly; and protein refolding. Located in cytosol and membrane. [provided by Alliance of Genome Resources, Apr 2022]

DNAJA4 links:

DNAJA4 (HGNC:):

DNAJA4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 15-78266242-CAT-C is Benign according to our data. Variant chr15-78266242-CAT-C is described in ClinVar as [Likely_benign]. Clinvar id is 402789.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJA4	NM_001130182.2 linkuse as main transcript	c.132+1348_132+1349delAT		intron_variant		ENST00000394852.8	NP_001123654.1	Q8WW22-1Q69YX3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJA4	ENST00000394852.8 linkuse as main transcript	c.132+1348_132+1349delAT		intron_variant		1	NM_001130182.2	ENSP00000378321.3		Q8WW22-1

Frequencies

GnomAD3 genomes

AF:

0.0296

AC:

4498

AN:

152182

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00668

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.0306

Gnomad ASJ

AF:

0.0568

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00849

Gnomad FIN

AF:

0.0396

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0436

Gnomad OTH

AF:

0.0401

GnomAD3 exomes

AF:

0.0323

AC:

8027

AN:

248720

Hom.:

200

AF XY:

0.0332

AC XY:

4484

AN XY:

135162

show subpopulations

Gnomad AFR exome

AF:

0.00603

Gnomad AMR exome

AF:

0.0228

Gnomad ASJ exome

AF:

0.0602

Gnomad EAS exome

AF:

0.000223

Gnomad SAS exome

AF:

0.0102

Gnomad FIN exome

AF:

0.0359

Gnomad NFE exome

AF:

0.0464

Gnomad OTH exome

AF:

0.0383

GnomAD4 exome

AF:

0.0377

AC:

55083

AN:

1461398

Hom.:

1257

AF XY:

0.0373

AC XY:

27096

AN XY:

726988

show subpopulations

Gnomad4 AFR exome

AF:

0.00687

Gnomad4 AMR exome

AF:

0.0242

Gnomad4 ASJ exome

AF:

0.0588

Gnomad4 EAS exome

AF:

0.000151

Gnomad4 SAS exome

AF:

0.0101

Gnomad4 FIN exome

AF:

0.0354

Gnomad4 NFE exome

AF:

0.0422

Gnomad4 OTH exome

AF:

0.0352

GnomAD4 genome

AF:

0.0295

AC:

4498

AN:

152300

Hom.:

Cov.:

AF XY:

0.0286

AC XY:

2126

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.00666

Gnomad4 AMR

AF:

0.0306

Gnomad4 ASJ

AF:

0.0568

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00850

Gnomad4 FIN

AF:

0.0396

Gnomad4 NFE

AF:

0.0436

Gnomad4 OTH

AF:

0.0397

Alfa

AF:

0.0125

Hom.:

Bravo

AF:

0.0292

Asia WGS

AF:

0.00664

AC:

AN:

3478

EpiCase

AF:

0.0514

EpiControl

AF:

0.0510

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in 1000Genomes:63/2178=2.89% -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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