1-6640071-CAAAAAA-CAAAAAAAAA

Position:

• chr1-6640071-CAAAAAA-CAAAAAAAAA

Variant summary

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

The NM_018198.4(DNAJC11):​c.1098-15_1098-14insTTT 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 0.000085 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00090 (0 hom.)
• Consequence: DNAJC11 NM_018198.4 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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAJC11	NM_018198.4	c.1098-15_1098-14insTTT		splice_polypyrimidine_tract_variant, intron_variant		ENST00000377577.10
DNAJC11	XM_047424842.1	c.828-15_828-14insTTT		splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAJC11	ENST00000377577.10	c.1098-15_1098-14insTTT		splice_polypyrimidine_tract_variant, intron_variant		1	NM_018198.4	P1

Frequencies

GnomAD3 genomes AF: 0.0000848 AC: 7 AN: 82516 Hom.: 0 Cov.: 0

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.: 0 Cov.: 0 AF XY: 0.00101 AC XY: 555 AN XY: 547996

Gnomad4 AFR exome AF: 0.000746

Gnomad4 AMR exome AF: 0.00247

Gnomad4 ASJ exome AF: 0.00176

Gnomad4 EAS exome AF: 0.00175

Gnomad4 SAS exome AF: 0.00406

Gnomad4 FIN exome AF: 0.00131

Gnomad4 NFE exome AF: 0.000641

Gnomad4 OTH exome AF: 0.00109

GnomAD4 genome AF: 0.0000849 AC: 7 AN: 82488 Hom.: 0 Cov.: 0 AF XY: 0.0000782 AC XY: 3 AN XY: 38380

Gnomad4 AFR AF: 0.000200

Gnomad4 AMR AF: 0.000137

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000343

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000239

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;