chr15-40768042-CCT-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018163.3(DNAJC17):c.811_812del(p.Arg271GlyfsTer98) variant causes a frameshift change. The variant allele was found at a frequency of 0.000017 in 1,584,120 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
DNAJC17
NM_018163.3 frameshift
NM_018163.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.82
Genes affected
DNAJC17 (HGNC:25556): (DnaJ heat shock protein family (Hsp40) member C17) Predicted to enable RNA binding activity. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II and toxin transport. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJC17 | NM_018163.3 | c.811_812del | p.Arg271GlyfsTer98 | frameshift_variant | 11/11 | ENST00000220496.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJC17 | ENST00000220496.9 | c.811_812del | p.Arg271GlyfsTer98 | frameshift_variant | 11/11 | 1 | NM_018163.3 | P1 | |
DNAJC17 | ENST00000558727.1 | n.376_377del | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
DNAJC17 | ENST00000561110.5 | n.358_359del | non_coding_transcript_exon_variant | 5/5 | 3 | ||||
DNAJC17 | ENST00000559238.5 | c.*839_*840del | 3_prime_UTR_variant, NMD_transcript_variant | 12/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152128Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000454 AC: 1AN: 220104Hom.: 0 AF XY: 0.00000840 AC XY: 1AN XY: 119084
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GnomAD4 exome AF: 0.0000168 AC: 24AN: 1431992Hom.: 0 AF XY: 0.0000155 AC XY: 11AN XY: 711042
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GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152128Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74314
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | May 09, 2023 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with DNAJC17-related conditions. This variant is present in population databases (rs773516322, gnomAD 0.001%). This sequence change results in a frameshift in the DNAJC17 gene (p.Arg271Glyfs*81). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 34 amino acid(s) of the DNAJC17 protein and extend the protein by 46 additional amino acid residues. - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at