rs12637073

Variant names:

• chr3-132464717-G-A
• rs12637073
• NM_015268.4:c.1892+900G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015268.4(DNAJC13):​c.1892+900G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,034 control chromosomes in the GnomAD database, including 1,432 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 0.10 (1432 hom., cov: 32)
• Consequence: DNAJC13 NM_015268.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 3 publications found

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 Gene-Disease associations (from GenCC):

• hereditary late onset Parkinson disease

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJC13	NM_015268.4	c.1892+900G>A		intron_variant	Intron 17 of 55	ENST00000260818.11	NP_056083.3
DNAJC13	NM_001329126.2	c.1892+900G>A		intron_variant	Intron 17 of 56		NP_001316055.1
DNAJC13	XM_047447819.1	c.1892+900G>A		intron_variant	Intron 17 of 56		XP_047303775.1
DNAJC13	XM_047447820.1	c.1892+900G>A		intron_variant	Intron 17 of 55		XP_047303776.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAJC13	ENST00000260818.11	c.1892+900G>A		intron_variant	Intron 17 of 55	1	NM_015268.4	ENSP00000260818.6
DNAJC13	ENST00000486798.5	n.1957+900G>A		intron_variant	Intron 17 of 19	1
DNAJC13	ENST00000650455.1	n.1892+900G>A		intron_variant	Intron 17 of 56			ENSP00000496825.1

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15294 AN: 151916 Hom.: 1436 Cov.: 32

Gnomad AFR AF: 0.0293

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0678

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0908

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

GnomAD4 genome AF: 0.101 AC: 15283 AN: 152034 Hom.: 1432 Cov.: 32 AF XY: 0.105 AC XY: 7803 AN XY: 74294

African (AFR) AF: 0.0292 AC: 1214 AN: 41530

American (AMR) AF: 0.0774 AC: 1183 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0678 AC: 235 AN: 3468

East Asian (EAS) AF: 0.534 AC: 2748 AN: 5148

South Asian (SAS) AF: 0.176 AC: 848 AN: 4822

European-Finnish (FIN) AF: 0.122 AC: 1290 AN: 10548

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7416 AN: 67928

Other (OTH) AF: 0.0894 AC: 188 AN: 2104

Alfa AF: 0.101 Hom.: 583

Bravo AF: 0.0936

Asia WGS AF: 0.284 AC: 982 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.17
PhyloP100		-0.071
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: rs12637073; hg19: chr3-132183561;