1-6640071-CAAAAAA-CAAAAA

Position:

• chr1-6640071-CAAAAAA-CAAAAA

Variant summary

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

The ENST00000377577.10(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 ENST00000377577.10 splice_polypyrimidine_tract, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

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]

ACMG classification

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	Protein	UniProt
DNAJC11	NM_018198.4	c.1098-15del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000377577.10	NP_060668.2
DNAJC11	XM_047424842.1	c.828-15del		splice_polypyrimidine_tract_variant, intron_variant			XP_047280798.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJC11	ENST00000377577.10	c.1098-15del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_018198.4	ENSP00000366800	P1

Frequencies

GnomAD3 genomes AF: 0.00842 AC: 695 AN: 82502 Hom.: 1 Cov.: 0

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.: 0 AF XY: 0.198 AC XY: 2630 AN XY: 13270

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.: 2 Cov.: 0 AF XY: 0.136 AC XY: 70005 AN XY: 513102

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.: 1 Cov.: 0 AF XY: 0.00860 AC XY: 330 AN XY: 38372

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

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

Other links and lift over

dbSNP: rs56145914; hg19: chr1-6700131;