Variant 1-6637225-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_018198.4(DNAJC11):c.1497G>A(p.Ser499Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00881 in 1,614,164 control chromosomes in the GnomAD database, including 97 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0059 ( 7 hom., cov: 33)

Exomes 𝑓: 0.0091 ( 90 hom. )

Consequence

DNAJC11
NM_018198.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.968

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 -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 1-6637225-C-T is Benign according to our data. Variant chr1-6637225-C-T is described in ClinVar as [Benign]. Clinvar id is 774784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.968 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJC11	NM_018198.4 linkuse as main transcript	c.1497G>A	p.Ser499Ser	synonymous_variant	14/16	ENST00000377577.10	NP_060668.2	Q9NVH1-1
DNAJC11	XM_047424842.1 linkuse as main transcript	c.1227G>A	p.Ser409Ser	synonymous_variant	12/14		XP_047280798.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJC11	ENST00000377577.10 linkuse as main transcript	c.1497G>A	p.Ser499Ser	synonymous_variant	14/16	1	NM_018198.4	ENSP00000366800.5		Q9NVH1-1

Frequencies

GnomAD3 genomes

AF:

0.00588

AC:

894

AN:

152166

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00135

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.00412

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00394

Gnomad FIN

AF:

0.0169

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00811

Gnomad OTH

AF:

0.00718

GnomAD3 exomes

AF:

0.00627

AC:

1576

AN:

251460

Hom.:

AF XY:

0.00655

AC XY:

890

AN XY:

135902

show subpopulations

Gnomad AFR exome

AF:

0.000923

Gnomad AMR exome

AF:

0.00301

Gnomad ASJ exome

AF:

0.00159

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00470

Gnomad FIN exome

AF:

0.0157

Gnomad NFE exome

AF:

0.00805

Gnomad OTH exome

AF:

0.00651

GnomAD4 exome

AF:

0.00912

AC:

13330

AN:

1461880

Hom.:

Cov.:

AF XY:

0.00891

AC XY:

6482

AN XY:

727236

show subpopulations

Gnomad4 AFR exome

AF:

0.00119

Gnomad4 AMR exome

AF:

0.00286

Gnomad4 ASJ exome

AF:

0.00207

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00533

Gnomad4 FIN exome

AF:

0.0149

Gnomad4 NFE exome

AF:

0.0102

Gnomad4 OTH exome

AF:

0.00843

GnomAD4 genome

AF:

0.00588

AC:

895

AN:

152284

Hom.:

Cov.:

AF XY:

0.00647

AC XY:

482

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.00135

Gnomad4 AMR

AF:

0.00412

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00415

Gnomad4 FIN

AF:

0.0169

Gnomad4 NFE

AF:

0.00812

Gnomad4 OTH

AF:

0.00710

Alfa

AF:

0.00733

Hom.:

Bravo

AF:

0.00486

Asia WGS

AF:

0.00260

AC:

AN:

3478

EpiCase

AF:

0.00747

EpiControl

AF:

0.00925

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	Labcorp Genetics (formerly Invitae), Labcorp	Jul 11, 2018	- -
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

-0.53

CADD

Benign

5.4

DANN

Benign

0.82

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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