Genetic Variant DNAJC11:c.1098-18_1098-15delTTTT (chr1-6640071-CAAAA-C) – 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.1098-18_1098-15delTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,217,382 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 0.000024 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00019 ( 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.1098-18_1098-15delTTTT		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.1098-18_1098-15delTTTT	intron	N/A	ENSP00000366800.5	Q9NVH1-1
DNAJC11	ENST00000294401.11	TSL:1	c.1098-1711_1098-1708delTTTT	intron	N/A	ENSP00000294401.7	Q9NVH1-3
DNAJC11	ENST00000451196.5	TSL:1	c.741-5291_741-5288delTTTT	intron	N/A	ENSP00000415871.1	Q5TH61

Frequencies

GnomAD3 genomes

AF:

0.0000242

AC:

AN:

82512

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000100

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:

0.000189

AC:

214

AN:

1134870

Hom.:

AF XY:

0.000212

AC XY:

116

AN XY:

547658

show subpopulations

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

African (AFR)

AF:

0.000166

AC:

AN:

24122

American (AMR)

AF:

0.000719

AC:

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.000326

AC:

AN:

15322

East Asian (EAS)

AF:

0.000439

AC:

AN:

27336

South Asian (SAS)

AF:

0.000180

AC:

AN:

49936

European-Finnish (FIN)

AF:

0.000614

AC:

AN:

24430

Middle Eastern (MID)

AF:

0.000329

AC:

AN:

3044

European-Non Finnish (NFE)

AF:

0.000151

AC:

140

AN:

929664

Other (OTH)

AF:

0.000372

AC:

AN:

45712

⚠️ 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: 0.253

Heterozygous variant carriers

116

145

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

AF:

0.0000242

AC:

AN:

82512

Hom.:

Cov.:

AF XY:

0.0000521

AC XY:

AN XY:

38370

show subpopulations

African (AFR)

AF:

0.000100

AC:

AN:

19988

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:

3144

Middle Eastern (MID)

AF:

0.00

AC:

AN:

186

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

41804

Other (OTH)

AF:

0.00

AC:

AN:

1118

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

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

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

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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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over