Variant chr7-108571909-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_012328.3(DNAJB9):c.183G>A(p.Pro61=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 1,613,686 control chromosomes in the GnomAD database, including 218,132 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.46 ( 17286 hom., cov: 32)

Exomes 𝑓: 0.52 ( 200846 hom. )

Consequence

DNAJB9
NM_012328.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.206

Variant links:

Genes affected

DNAJB9 (HGNC:6968): (DnaJ heat shock protein family (Hsp40) member B9) This gene is a member of the J protein family. J proteins function in many cellular processes by regulating the ATPase activity of 70 kDa heat shock proteins. This gene is a member of the type 2 subgroup of DnaJ proteins. The encoded protein is localized to the endoplasmic reticulum. This protein is induced by endoplasmic reticulum stress and plays a role in protecting stressed cells from apoptosis. [provided by RefSeq, Dec 2010]

DNAJB9 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP7

Synonymous conserved (PhyloP=0.206 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAJB9	NM_012328.3 linkuse as main transcript	c.183G>A	p.Pro61=	synonymous_variant	2/3	ENST00000249356.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
DNAJB9	ENST00000249356.4 linkuse as main transcript	c.183G>A	p.Pro61=	synonymous_variant	2/3	1	NM_012328.3	P1
DNAJB9	ENST00000465725.1 linkuse as main transcript	n.195G>A		non_coding_transcript_exon_variant	1/2	2
DNAJB9	ENST00000491582.1 linkuse as main transcript	n.430G>A		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.465

AC:

70540

AN:

151838

Hom.:

17275

Cov.:

show subpopulations

Gnomad AFR

AF:

0.301

Gnomad AMI

AF:

0.447

Gnomad AMR

AF:

0.565

Gnomad ASJ

AF:

0.423

Gnomad EAS

AF:

0.599

Gnomad SAS

AF:

0.506

Gnomad FIN

AF:

0.546

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.519

Gnomad OTH

AF:

0.459

GnomAD3 exomes

AF:

0.523

AC:

131515

AN:

251372

Hom.:

35311

AF XY:

0.522

AC XY:

70988

AN XY:

135870

show subpopulations

Gnomad AFR exome

AF:

0.299

Gnomad AMR exome

AF:

0.629

Gnomad ASJ exome

AF:

0.425

Gnomad EAS exome

AF:

0.613

Gnomad SAS exome

AF:

0.524

Gnomad FIN exome

AF:

0.534

Gnomad NFE exome

AF:

0.515

Gnomad OTH exome

AF:

0.515

GnomAD4 exome

AF:

0.522

AC:

762859

AN:

1461730

Hom.:

200846

Cov.:

AF XY:

0.522

AC XY:

379451

AN XY:

727168

show subpopulations

Gnomad4 AFR exome

AF:

0.292

Gnomad4 AMR exome

AF:

0.618

Gnomad4 ASJ exome

AF:

0.430

Gnomad4 EAS exome

AF:

0.601

Gnomad4 SAS exome

AF:

0.522

Gnomad4 FIN exome

AF:

0.531

Gnomad4 NFE exome

AF:

0.525

Gnomad4 OTH exome

AF:

0.509

GnomAD4 genome

AF:

0.464

AC:

70568

AN:

151956

Hom.:

17286

Cov.:

AF XY:

0.470

AC XY:

34928

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.300

Gnomad4 AMR

AF:

0.566

Gnomad4 ASJ

AF:

0.423

Gnomad4 EAS

AF:

0.598

Gnomad4 SAS

AF:

0.506

Gnomad4 FIN

AF:

0.546

Gnomad4 NFE

AF:

0.519

Gnomad4 OTH

AF:

0.453

Alfa

AF:

0.497

Hom.:

33998

Bravo

AF:

0.458

Asia WGS

AF:

0.484

AC:

1686

AN:

3478

EpiCase

AF:

0.509

EpiControl

AF:

0.503

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

7.7

DANN

Benign

0.82

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over