Variant 1-6640071-CAAAAAA-CAAAAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_018198.4(DNAJC11):c.1098-15del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0084 ( 1 hom., cov: 0)

Exomes 𝑓: 0.14 ( 2 hom. )

Consequence

DNAJC11
NM_018198.4 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.23

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAJC11	NM_018198.4 linkuse as main transcript	c.1098-15del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000377577.10
DNAJC11	XM_047424842.1 linkuse as main transcript	c.828-15del		splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAJC11	ENST00000377577.10 linkuse as main transcript	c.1098-15del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_018198.4	P1	Q9NVH1-1

Frequencies

GnomAD3 genomes

AF:

0.00842

AC:

695

AN:

82502

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0160

Gnomad AMI

AF:

0.0290

Gnomad AMR

AF:

0.00576

Gnomad ASJ

AF:

0.000838

Gnomad EAS

AF:

0.000923

Gnomad SAS

AF:

0.000681

Gnomad FIN

AF:

0.00828

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00667

Gnomad OTH

AF:

0.00804

GnomAD3 exomes

AF:

0.202

AC:

5347

AN:

26422

Hom.:

AF XY:

0.198

AC XY:

2630

AN XY:

13270

show subpopulations

Gnomad AFR exome

AF:

0.232

Gnomad AMR exome

AF:

0.226

Gnomad ASJ exome

AF:

0.169

Gnomad EAS exome

AF:

0.175

Gnomad SAS exome

AF:

0.153

Gnomad FIN exome

AF:

0.131

Gnomad NFE exome

AF:

0.218

Gnomad OTH exome

AF:

0.169

GnomAD4 exome

AF:

0.137

AC:

145169

AN:

1062594

Hom.:

Cov.:

AF XY:

0.136

AC XY:

70005

AN XY:

513102

show subpopulations

Gnomad4 AFR exome

AF:

0.168

Gnomad4 AMR exome

AF:

0.183

Gnomad4 ASJ exome

AF:

0.160

Gnomad4 EAS exome

AF:

0.166

Gnomad4 SAS exome

AF:

0.100

Gnomad4 FIN exome

AF:

0.208

Gnomad4 NFE exome

AF:

0.133

Gnomad4 OTH exome

AF:

0.149

GnomAD4 genome

AF:

0.00844

AC:

696

AN:

82474

Hom.:

Cov.:

AF XY:

0.00860

AC XY:

330

AN XY:

38372

show subpopulations

Gnomad4 AFR

AF:

0.0160

Gnomad4 AMR

AF:

0.00576

Gnomad4 ASJ

AF:

0.000838

Gnomad4 EAS

AF:

0.000928

Gnomad4 SAS

AF:

0.000685

Gnomad4 FIN

AF:

0.00828

Gnomad4 NFE

AF:

0.00668

Gnomad4 OTH

AF:

0.00795

ClinVar

Not reported in ClinVar

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over