rs9594865

chr13-43024276-G-Achr13-43024276-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013238.3(DNAJC15):c.108+542G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 151,244 control chromosomes in the GnomAD database, including 3,768 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.22 (3768 hom., cov: 30)
• Consequence: DNAJC15 NM_013238.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

Genes affected

DNAJC15 (HGNC:20325): (DnaJ heat shock protein family (Hsp40) member C15) Predicted to enable ATPase activator activity. Predicted to be involved in protein import into mitochondrial matrix. Predicted to act upstream of or within several processes, including cellular response to starvation; negative regulation of mitochondrial electron transport, NADH to ubiquinone; and negative regulation of protein-containing complex assembly. Predicted to be located in mitochondrial inner membrane. Predicted to be part of PAM complex, Tim23 associated import motor. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAJC15	NM_013238.3	c.108+542G>A		intron_variant		ENST00000379221.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAJC15	ENST00000379221.4	c.108+542G>A		intron_variant		1	NM_013238.3	P1
DNAJC15	ENST00000474320.1	n.532+542G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33544 AN: 151136 Hom.: 3762 Cov.: 30

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.0888

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.217

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.222 AC: 33577 AN: 151244 Hom.: 3768 Cov.: 30 AF XY: 0.218 AC XY: 16090 AN XY: 73814

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.0892

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.219

Alfa AF: 0.173 Hom.: 466

Bravo AF: 0.218

Asia WGS AF: 0.140 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.77
Dann	Benign	0.76

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: rs9594865; hg19: chr13-43598412;