3-132434331-AGCAAAGATCGTGC-A

Position:

• chr3-132434331-AGCAAAGATCGTGC-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_015268.4(DNAJC13):​c.-13-206_-13-194delGCAAAGATCGTGC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0458 in 151,442 control chromosomes in the GnomAD database, including 487 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.046 (487 hom., cov: 29)
• Consequence: DNAJC13 NM_015268.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.560

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]

DNAJC13 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-132434331-AGCAAAGATCGTGC-A is Benign according to our data. Variant chr3-132434331-AGCAAAGATCGTGC-A is described in ClinVar as [Benign]. Clinvar id is 1230766.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJC13	NM_015268.4	c.-13-206_-13-194delGCAAAGATCGTGC		intron_variant		ENST00000260818.11	NP_056083.3
DNAJC13	NM_001329126.2	c.-13-206_-13-194delGCAAAGATCGTGC		intron_variant			NP_001316055.1
DNAJC13	XM_047447819.1	c.-13-206_-13-194delGCAAAGATCGTGC		intron_variant			XP_047303775.1
DNAJC13	XM_047447820.1	c.-13-206_-13-194delGCAAAGATCGTGC		intron_variant			XP_047303776.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJC13	ENST00000260818.11	c.-13-206_-13-194delGCAAAGATCGTGC		intron_variant		1	NM_015268.4	ENSP00000260818.6
DNAJC13	ENST00000486798.5	n.53-206_53-194delGCAAAGATCGTGC		intron_variant		1
DNAJC13	ENST00000650455.1	n.-13-206_-13-194delGCAAAGATCGTGC		intron_variant				ENSP00000496825.1

Frequencies

GnomAD3 genomes AF: 0.0458 AC: 6927 AN: 151338 Hom.: 486 Cov.: 29

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0201

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.0299

Gnomad SAS AF: 0.00229

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.00102

Gnomad OTH AF: 0.0371

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

GnomAD4 genome AF: 0.0458 AC: 6938 AN: 151442 Hom.: 487 Cov.: 29 AF XY: 0.0436 AC XY: 3232 AN XY: 74060

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.0200

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.0295

Gnomad4 SAS AF: 0.00187

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00102

Gnomad4 OTH AF: 0.0371

Alfa AF: 0.0441 Hom.: 37

Asia WGS AF: 0.0230 AC: 80 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 14, 2018

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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: rs144868266; hg19: chr3-132153175;