13-43029735-C-T

Variant names:

• chr13-43029735-C-T
• rs1323862
• NM_013238.3:c.108+6001C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013238.3. 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
	DNAJC15	NM_013238.3	MANE Select	c.108+6001C>T		intron	N/A	NP_037370.2	Q9Y5T4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJC15	ENST00000379221.4	TSL:1 MANE Select	c.108+6001C>T		intron	N/A	ENSP00000368523.2	Q9Y5T4
	DNAJC15	ENST00000885099.1		c.108+6001C>T		intron	N/A	ENSP00000555158.1
	DNAJC15	ENST00000885100.1		c.108+6001C>T		intron	N/A	ENSP00000555159.1

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

African (AFR) AF: 0.619 AC: 25620 AN: 41380

American (AMR) AF: 0.567 AC: 8654 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1696 AN: 3466

East Asian (EAS) AF: 0.409 AC: 2090 AN: 5110

South Asian (SAS) AF: 0.545 AC: 2624 AN: 4814

European-Finnish (FIN) AF: 0.539 AC: 5651 AN: 10484

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.540 AC: 36642 AN: 67892

Other (OTH) AF: 0.550 AC: 1153 AN: 2098

Alfa AF: 0.546 Hom.: 11476

Bravo AF: 0.565

Asia WGS AF: 0.490 AC: 1708 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.0
DANN	Benign	0.70
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1323862; hg19: chr13-43603871;