rs2369796
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015268.4(DNAJC13):c.2550-9A>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 1,551,476 control chromosomes in the GnomAD database, including 170,597 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.61 ( 31126 hom., cov: 29)
Exomes 𝑓: 0.47 ( 139471 hom. )
Consequence
DNAJC13
NM_015268.4 splice_polypyrimidine_tract, intron
NM_015268.4 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00003163
2
Clinical Significance
Conservation
PhyloP100: 0.0150
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 3-132477972-A-T is Benign according to our data. Variant chr3-132477972-A-T is described in ClinVar as [Benign]. Clinvar id is 1210029.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-132477972-A-T is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJC13 | NM_015268.4 | c.2550-9A>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000260818.11 | |||
DNAJC13 | NM_001329126.2 | c.2565-9A>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
DNAJC13 | XM_047447819.1 | c.2565-9A>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
DNAJC13 | XM_047447820.1 | c.2550-9A>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJC13 | ENST00000260818.11 | c.2550-9A>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_015268.4 | P1 | |||
DNAJC13 | ENST00000650455.1 | c.*698-9A>T | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | ||||||
DNAJC13 | ENST00000464766.1 | n.387-9A>T | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.614 AC: 92339AN: 150374Hom.: 31068 Cov.: 29
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GnomAD3 exomes AF: 0.481 AC: 100248AN: 208392Hom.: 21004 AF XY: 0.473 AC XY: 53555AN XY: 113196
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GnomAD4 exome AF: 0.466 AC: 653314AN: 1400998Hom.: 139471 Cov.: 35 AF XY: 0.468 AC XY: 325580AN XY: 696168
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GnomAD4 genome AF: 0.614 AC: 92452AN: 150478Hom.: 31126 Cov.: 29 AF XY: 0.615 AC XY: 45173AN XY: 73460
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2018 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at