Genetic Variant NM_018198.4:c.1098-26_1098-15dupTTTTTTTTTTTT (chr1-6640071-C-CAAAAAAAAAAAA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_018198.4(DNAJC11):c.1098-26_1098-15dupTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 0)

Exomes 𝑓: 8.8e-7 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

DNAJC11
NM_018198.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.23

Publications

0 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018198.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJC11	NM_018198.4	MANE Select	c.1098-26_1098-15dupTTTTTTTTTTTT		intron	N/A	NP_060668.2	Q9NVH1-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DNAJC11	ENST00000377577.10	TSL:1 MANE Select	c.1098-15_1098-14insTTTTTTTTTTTT	intron	N/A	ENSP00000366800.5	Q9NVH1-1
DNAJC11	ENST00000294401.11	TSL:1	c.1098-1708_1098-1707insTTTTTTTTTTTT	intron	N/A	ENSP00000294401.7	Q9NVH1-3
DNAJC11	ENST00000451196.5	TSL:1	c.741-5288_741-5287insTTTTTTTTTTTT	intron	N/A	ENSP00000415871.1	Q5TH61

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

82518

Hom.:

Cov.:

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:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

8.80e-7

AC:

AN:

1136542

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

548502

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00

AC:

AN:

24168

American (AMR)

AF:

0.00

AC:

AN:

15368

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15364

East Asian (EAS)

AF:

0.00

AC:

AN:

27428

South Asian (SAS)

AF:

0.00

AC:

AN:

50048

European-Finnish (FIN)

AF:

0.00

AC:

AN:

24512

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3046

European-Non Finnish (NFE)

AF:

0.00000107

AC:

AN:

930802

Other (OTH)

AF:

0.00

AC:

AN:

45806

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.325

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

82518

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

38372

African (AFR)

AF:

0.00

AC:

AN:

19990

American (AMR)

AF:

0.00

AC:

AN:

7286

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2386

East Asian (EAS)

AF:

0.00

AC:

AN:

3250

South Asian (SAS)

AF:

0.00

AC:

AN:

2936

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3146

Middle Eastern (MID)

AF:

0.00

AC:

AN:

186

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

41806

Other (OTH)

AF:

0.00

AC:

AN:

1118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over