Genetic Variant DNAJC11:c.1098-17_1098-15delTTT (chr1-6640071-CAAA-C) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_018198.4(DNAJC11):c.1098-17_1098-15delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00111 in 1,212,668 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000048 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0012 ( 0 hom. )

Consequence

DNAJC11
NM_018198.4 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 Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJC11	NM_018198.4 link	c.1098-17_1098-15delTTT		intron_variant	Intron 10 of 15	ENST00000377577.10	NP_060668.2	Q9NVH1-1
DNAJC11	XM_047424842.1 link	c.828-17_828-15delTTT		intron_variant	Intron 8 of 13		XP_047280798.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAJC11	ENST00000377577.10 link	c.1098-17_1098-15delTTT		intron_variant	Intron 10 of 15	1	NM_018198.4	ENSP00000366800.5		Q9NVH1-1

Frequencies

GnomAD3 genomes

AF:

0.0000485

AC:

AN:

82514

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000957

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00549

AC:

145

AN:

26422

Hom.:

AF XY:

0.00528

AC XY:

AN XY:

13270

show subpopulations

Gnomad AFR exome

AF:

0.00366

Gnomad AMR exome

AF:

0.00636

Gnomad ASJ exome

AF:

0.00884

Gnomad EAS exome

AF:

0.00418

Gnomad SAS exome

AF:

0.00373

Gnomad FIN exome

AF:

0.00437

Gnomad NFE exome

AF:

0.00656

Gnomad OTH exome

AF:

0.00355

GnomAD4 exome

AF:

0.00118

AC:

1336

AN:

1130182

Hom.:

AF XY:

0.00122

AC XY:

665

AN XY:

545344

show subpopulations

Gnomad4 AFR exome

AF:

0.00204

Gnomad4 AMR exome

AF:

0.00442

Gnomad4 ASJ exome

AF:

0.00269

Gnomad4 EAS exome

AF:

0.00243

Gnomad4 SAS exome

AF:

0.00119

Gnomad4 FIN exome

AF:

0.00347

Gnomad4 NFE exome

AF:

0.000953

Gnomad4 OTH exome

AF:

0.00178

GnomAD4 genome

AF:

0.0000485

AC:

AN:

82486

Hom.:

Cov.:

AF XY:

0.0000782

AC XY:

AN XY:

38378

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000957

Gnomad4 OTH

AF:

0.00

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.

1-6640071-CAAAAAA-CAAA

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