3-132434384-CAAA-CAA

Variant names:

• chr3-132434384-CA-C
• rs761665933
• NM_015268.4:c.-13-140delA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_015268.4(DNAJC13):​c.-13-140delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000995 in 94,490 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.00099 (0 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 94 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJC13	NM_015268.4	c.-13-140delA		intron_variant	Intron 1 of 55	ENST00000260818.11	NP_056083.3
DNAJC13	NM_001329126.2	c.-13-140delA		intron_variant	Intron 1 of 56		NP_001316055.1
DNAJC13	XM_047447819.1	c.-13-140delA		intron_variant	Intron 1 of 56		XP_047303775.1
DNAJC13	XM_047447820.1	c.-13-140delA		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.-13-153delA		intron_variant	Intron 1 of 55	1	NM_015268.4	ENSP00000260818.6
DNAJC13	ENST00000486798.5	n.53-153delA		intron_variant	Intron 1 of 19	1
DNAJC13	ENST00000650455.1	n.-13-153delA		intron_variant	Intron 1 of 56			ENSP00000496825.1

Frequencies

GnomAD3 genomes AF: 0.000995 AC: 94 AN: 94458 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000769

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000461

Gnomad ASJ AF: 0.000875

Gnomad EAS AF: 0.000927

Gnomad SAS AF: 0.000744

Gnomad FIN AF: 0.00665

Gnomad MID AF: 0.00556

Gnomad NFE AF: 0.000663

Gnomad OTH AF: 0.00161

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

GnomAD4 genome AF: 0.000995 AC: 94 AN: 94490 Hom.: 0 Cov.: 31 AF XY: 0.00114 AC XY: 51 AN XY: 44734

Gnomad4 AFR AF: 0.000767

Gnomad4 AMR AF: 0.000461

Gnomad4 ASJ AF: 0.000875

Gnomad4 EAS AF: 0.000929

Gnomad4 SAS AF: 0.000747

Gnomad4 FIN AF: 0.00665

Gnomad4 NFE AF: 0.000664

Gnomad4 OTH AF: 0.00161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs761665933; hg19: chr3-132153228;