3-132446211-T-A

Position:

• chr3-132446211-T-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_015268.4(DNAJC13):​c.69-264T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 151,600 control chromosomes in the GnomAD database, including 20,230 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.50 (20230 hom., cov: 31)
• Consequence: DNAJC13 NM_015268.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.11

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 3-132446211-T-A is Benign according to our data. Variant chr3-132446211-T-A is described in ClinVar as [Benign]. Clinvar id is 1263992.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAJC13	NM_015268.4	c.69-264T>A		intron_variant		ENST00000260818.11	NP_056083.3
DNAJC13	NM_001329126.2	c.69-264T>A		intron_variant			NP_001316055.1
DNAJC13	XM_047447819.1	c.69-264T>A		intron_variant			XP_047303775.1
DNAJC13	XM_047447820.1	c.69-264T>A		intron_variant			XP_047303776.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAJC13	ENST00000260818.11	c.69-264T>A		intron_variant		1	NM_015268.4	ENSP00000260818.6
DNAJC13	ENST00000486798.5	n.134-264T>A		intron_variant		1
DNAJC13	ENST00000650455.1	n.69-264T>A		intron_variant				ENSP00000496825.1

Frequencies

GnomAD3 genomes AF: 0.501 AC: 75896 AN: 151484 Hom.: 20187 Cov.: 31

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.501 AC: 75983 AN: 151600 Hom.: 20230 Cov.: 31 AF XY: 0.507 AC XY: 37508 AN XY: 74036

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.454

Alfa AF: 0.271 Hom.: 562

Bravo AF: 0.510

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

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.44
DANN	Benign	0.30

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: rs1979847; hg19: chr3-132165055;