NM_015268.4:c.-13-141_-13-140dupAA

Variant names:

• chr3-132434384-C-CAA
• rs761665933
• NM_015268.4:c.-13-141_-13-140dupAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_015268.4(DNAJC13):​c.-13-141_-13-140dupAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0237 in 94,440 control chromosomes in the GnomAD database, including 30 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.024 (30 hom., cov: 31)
• Consequence: DNAJC13 NM_015268.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950

Genes affected

DNAJC13 (HGNC:30343): (DnaJ heat shock protein family (Hsp40) member C13) This gene encodes a member of the Dnaj protein family whose members act as co-chaperones of a partner heat-shock protein by binding to the latter and stimulating ATP hydrolysis. The encoded protein associates with the heat-shock protein Hsc70 and plays a role in clathrin-mediated endocytosis. It may also be involved in post-endocytic transport mechanisms via its associations with other proteins, including the sorting nexin SNX1. Mutations in this gene are associated with Parkinson's disease. [provided by RefSeq, Jun 2016]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0237 (2237/94440) while in subpopulation NFE AF= 0.0363 (1587/43678). AF 95% confidence interval is 0.0348. There are 30 homozygotes in gnomad4. There are 993 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 2237 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJC13	NM_015268.4	c.-13-141_-13-140dupAA		intron_variant	Intron 1 of 55	ENST00000260818.11	NP_056083.3
DNAJC13	NM_001329126.2	c.-13-141_-13-140dupAA		intron_variant	Intron 1 of 56		NP_001316055.1
DNAJC13	XM_047447819.1	c.-13-141_-13-140dupAA		intron_variant	Intron 1 of 56		XP_047303775.1
DNAJC13	XM_047447820.1	c.-13-141_-13-140dupAA		intron_variant	Intron 1 of 55		XP_047303776.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAJC13	ENST00000260818.11	c.-13-154_-13-153insAA		intron_variant	Intron 1 of 55	1	NM_015268.4	ENSP00000260818.6
DNAJC13	ENST00000486798.5	n.53-154_53-153insAA		intron_variant	Intron 1 of 19	1
DNAJC13	ENST00000650455.1	n.-13-154_-13-153insAA		intron_variant	Intron 1 of 56			ENSP00000496825.1

Frequencies

GnomAD3 genomes AF: 0.0237 AC: 2239 AN: 94408 Hom.: 30 Cov.: 31

Gnomad AFR AF: 0.00681

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0266

Gnomad ASJ AF: 0.0105

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00521

Gnomad FIN AF: 0.0148

Gnomad MID AF: 0.0278

Gnomad NFE AF: 0.0364

Gnomad OTH AF: 0.0242

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

GnomAD4 genome AF: 0.0237 AC: 2237 AN: 94440 Hom.: 30 Cov.: 31 AF XY: 0.0222 AC XY: 993 AN XY: 44714

Gnomad4 AFR AF: 0.00680

Gnomad4 AMR AF: 0.0265

Gnomad4 ASJ AF: 0.0105

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00523

Gnomad4 FIN AF: 0.0148

Gnomad4 NFE AF: 0.0363

Gnomad4 OTH AF: 0.0242

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: rs761665933; hg19: chr3-132153228;