3-132434489-T-TAG

Position:

• chr3-132434489-T-TAG

Variant summary

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

The NM_015268.4(DNAJC13):​c.-13-49_-13-48insAG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.30 (7889 hom., cov: 11)
  • Exomes 𝑓: 0.22 (30846 hom.)
• Consequence: DNAJC13 NM_015268.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.747

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 3-132434489-T-TAG is Benign according to our data. Variant chr3-132434489-T-TAG is described in ClinVar as [Benign]. Clinvar id is 1293955.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJC13	NM_015268.4	c.-13-49_-13-48insAG		intron_variant		ENST00000260818.11	NP_056083.3
DNAJC13	NM_001329126.2	c.-13-49_-13-48insAG		intron_variant			NP_001316055.1
DNAJC13	XM_047447819.1	c.-13-49_-13-48insAG		intron_variant			XP_047303775.1
DNAJC13	XM_047447820.1	c.-13-49_-13-48insAG		intron_variant			XP_047303776.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJC13	ENST00000260818.11	c.-13-49_-13-48insAG		intron_variant		1	NM_015268.4	ENSP00000260818.6
DNAJC13	ENST00000486798.5	n.53-49_53-48insAG		intron_variant		1
DNAJC13	ENST00000650455.1	n.-13-49_-13-48insAG		intron_variant				ENSP00000496825.1

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44806 AN: 151788 Hom.: 7854 Cov.: 11

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.267

GnomAD4 exome AF: 0.218 AC: 261504 AN: 1199872 Hom.: 30846 Cov.: 15 AF XY: 0.219 AC XY: 133178 AN XY: 607918

Gnomad4 AFR exome AF: 0.503

Gnomad4 AMR exome AF: 0.258

Gnomad4 ASJ exome AF: 0.234

Gnomad4 EAS exome AF: 0.215

Gnomad4 SAS exome AF: 0.292

Gnomad4 FIN exome AF: 0.180

Gnomad4 NFE exome AF: 0.203

Gnomad4 OTH exome AF: 0.237

GnomAD4 genome AF: 0.296 AC: 44909 AN: 151904 Hom.: 7889 Cov.: 11 AF XY: 0.294 AC XY: 21857 AN XY: 74280

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.271

Alfa AF: 0.260 Hom.: 713

Bravo AF: 0.313

Asia WGS AF: 0.332 AC: 1152 AN: 3478

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 09, 2018

- -

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: rs10662251; hg19: chr3-132153333;