Genetic Variant DNAJC11:c.1098-17_1098-15dupTTT (chr1-6640071-C-CAAA) – 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.1098-17_1098-15dupTTT variant causes a 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 0.000085 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00090 ( 0 hom. )

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.1098-17_1098-15dupTTT		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_1098-14insTTT	intron	N/A	ENSP00000366800.5	Q9NVH1-1
DNAJC11	ENST00000294401.11	TSL:1	c.1098-1708_1098-1707insTTT	intron	N/A	ENSP00000294401.7	Q9NVH1-3
DNAJC11	ENST00000451196.5	TSL:1	c.741-5288_741-5287insTTT	intron	N/A	ENSP00000415871.1	Q5TH61

Frequencies

GnomAD3 genomes

AF:

0.0000848

AC:

AN:

82516

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000200

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000137

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000341

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000239

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000897

AC:

1019

AN:

1135446

Hom.:

Cov.:

AF XY:

0.00101

AC XY:

555

AN XY:

547996

show subpopulations

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

African (AFR)

AF:

0.000746

AC:

AN:

24144

American (AMR)

AF:

0.00247

AC:

AN:

15358

Ashkenazi Jewish (ASJ)

AF:

0.00176

AC:

AN:

15336

East Asian (EAS)

AF:

0.00175

AC:

AN:

27386

South Asian (SAS)

AF:

0.00406

AC:

203

AN:

49996

European-Finnish (FIN)

AF:

0.00131

AC:

AN:

24488

Middle Eastern (MID)

AF:

0.00230

AC:

AN:

3042

European-Non Finnish (NFE)

AF:

0.000641

AC:

596

AN:

929924

Other (OTH)

AF:

0.00109

AC:

AN:

45772

⚠️ 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: 0.324

Heterozygous variant carriers

130

194

259

324

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

100

<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

AF:

0.0000849

AC:

AN:

82488

Hom.:

Cov.:

AF XY:

0.0000782

AC XY:

AN XY:

38380

show subpopulations

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

African (AFR)

AF:

0.000200

AC:

AN:

20012

American (AMR)

AF:

0.000137

AC:

AN:

7290

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2386

East Asian (EAS)

AF:

0.00

AC:

AN:

3234

South Asian (SAS)

AF:

0.000343

AC:

AN:

2918

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3146

Middle Eastern (MID)

AF:

0.00

AC:

AN:

164

European-Non Finnish (NFE)

AF:

0.0000239

AC:

AN:

41794

Other (OTH)

AF:

0.00

AC:

AN:

1130

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000286740), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.368

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome 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

Alfa

AF:

0.00

Hom.:

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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1-6640071-CAAAAAA-CAAAAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over