rs1323862

Positions:

• chr13-43029735-C-T

Variant summary

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

The NM_013238.3(DNAJC15):​c.108+6001C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,698 control chromosomes in the GnomAD database, including 23,851 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 0.56 (23851 hom., cov: 32)
• Consequence: DNAJC15 NM_013238.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAJC15	NM_013238.3	c.108+6001C>T		intron_variant		ENST00000379221.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAJC15	ENST00000379221.4	c.108+6001C>T		intron_variant		1	NM_013238.3	P1
DNAJC15	ENST00000474320.1	n.532+6001C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84924 AN: 151580 Hom.: 23832 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.560 AC: 84988 AN: 151698 Hom.: 23851 Cov.: 32 AF XY: 0.559 AC XY: 41454 AN XY: 74094

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.550

Alfa AF: 0.547 Hom.: 10375

Bravo AF: 0.565

Asia WGS AF: 0.490 AC: 1708 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.0
DANN	Benign	0.70

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: rs1323862; hg19: chr13-43603871;