Variant rs12137794 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018198.4(DNAJC11):c.799G>A(p.Val267Met) variant causes a missense change. The variant allele was found at a frequency of 0.0787 in 1,614,104 control chromosomes in the GnomAD database, including 5,510 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.064 ( 424 hom., cov: 32)

Exomes 𝑓: 0.080 ( 5086 hom. )

Consequence

DNAJC11
NM_018198.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.66

Variant links:

Genes affected

DNAJC11 (HGNC:25570): (DnaJ heat shock protein family (Hsp40) member C11) Involved in cristae formation. Located in mitochondrial outer membrane and nuclear speck. Part of MIB complex. Colocalizes with MICOS complex and SAM complex. [provided by Alliance of Genome Resources, Apr 2022]

DNAJC11 links:

DNAJC11 (HGNC:):

DNAJC11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0021018386).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJC11	NM_018198.4 linkuse as main transcript	c.799G>A	p.Val267Met	missense_variant	8/16	ENST00000377577.10	NP_060668.2	Q9NVH1-1
DNAJC11	XM_047424842.1 linkuse as main transcript	c.529G>A	p.Val177Met	missense_variant	6/14		XP_047280798.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJC11	ENST00000377577.10 linkuse as main transcript	c.799G>A	p.Val267Met	missense_variant	8/16	1	NM_018198.4	ENSP00000366800.5		Q9NVH1-1

Frequencies

GnomAD3 genomes

AF:

0.0636

AC:

9669

AN:

152120

Hom.:

423

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0154

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.0967

Gnomad ASJ

AF:

0.0602

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0483

Gnomad FIN

AF:

0.0993

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0866

Gnomad OTH

AF:

0.0664

GnomAD3 exomes

AF:

0.0732

AC:

18409

AN:

251482

Hom.:

846

AF XY:

0.0729

AC XY:

9913

AN XY:

135918

show subpopulations

Gnomad AFR exome

AF:

0.0125

Gnomad AMR exome

AF:

0.111

Gnomad ASJ exome

AF:

0.0632

Gnomad EAS exome

AF:

0.000272

Gnomad SAS exome

AF:

0.0498

Gnomad FIN exome

AF:

0.102

Gnomad NFE exome

AF:

0.0838

Gnomad OTH exome

AF:

0.0725

GnomAD4 exome

AF:

0.0803

AC:

117327

AN:

1461866

Hom.:

5086

Cov.:

AF XY:

0.0797

AC XY:

57969

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.0125

Gnomad4 AMR exome

AF:

0.115

Gnomad4 ASJ exome

AF:

0.0672

Gnomad4 EAS exome

AF:

0.000227

Gnomad4 SAS exome

AF:

0.0524

Gnomad4 FIN exome

AF:

0.102

Gnomad4 NFE exome

AF:

0.0861

Gnomad4 OTH exome

AF:

0.0680

GnomAD4 genome

AF:

0.0636

AC:

9677

AN:

152238

Hom.:

424

Cov.:

AF XY:

0.0643

AC XY:

4786

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.0153

Gnomad4 AMR

AF:

0.0969

Gnomad4 ASJ

AF:

0.0602

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.0492

Gnomad4 FIN

AF:

0.0993

Gnomad4 NFE

AF:

0.0866

Gnomad4 OTH

AF:

0.0653

Alfa

AF:

0.0776

Hom.:

1266

Bravo

AF:

0.0590

TwinsUK

AF:

0.0885

AC:

328

ALSPAC

AF:

0.0869

AC:

335

ESP6500AA

AF:

0.0170

AC:

ESP6500EA

AF:

0.0823

AC:

708

ExAC

AF:

0.0692

AC:

8406

Asia WGS

AF:

0.0210

AC:

AN:

3478

EpiCase

AF:

0.0748

EpiControl

AF:

0.0759

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.069

BayesDel_addAF

Benign

-0.59

BayesDel_noAF

Benign

-0.53

CADD

Benign

DANN

Benign

0.88

DEOGEN2

Benign

0.013

.;T;.;.

Eigen

Benign

-0.18

Eigen_PC

Benign

0.054

FATHMM_MKL

Uncertain

0.77

LIST_S2

Uncertain

0.88

D;D;D;D

MetaRNN

Benign

0.0021

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-1.2

.;N;N;.

PrimateAI

Uncertain

0.50

PROVEAN

Benign

-0.28

N;N;N;N

REVEL

Benign

0.093

Sift

Benign

0.27

T;T;T;T

Sift4G

Benign

0.38

T;T;T;.

Polyphen

0.22

B;B;B;.

Vest4

0.097, 0.058

MPC

0.48

ClinPred

0.019

GERP RS

4.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.053

gMVP

0.21

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