chr5-34929869-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001012339.3(DNAJC21):c.50A>T(p.Glu17Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000281 in 1,421,744 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E17G) has been classified as Likely benign.
Frequency
Consequence
NM_001012339.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJC21 | NM_001012339.3 | c.50A>T | p.Glu17Val | missense_variant | 1/12 | ENST00000648817.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJC21 | ENST00000648817.1 | c.50A>T | p.Glu17Val | missense_variant | 1/12 | NM_001012339.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 29
GnomAD3 exomes AF: 0.00000909 AC: 2AN: 219976Hom.: 0 AF XY: 0.0000166 AC XY: 2AN XY: 120714
GnomAD4 exome AF: 0.00000281 AC: 4AN: 1421744Hom.: 0 Cov.: 31 AF XY: 0.00000283 AC XY: 2AN XY: 707524
GnomAD4 genome ? Cov.: 29
ClinVar
Submissions by phenotype
DNAJC21-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 29, 2023 | The DNAJC21 c.50A>T variant is predicted to result in the amino acid substitution p.Glu17Val. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0010% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/5-34929974-A-T). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2024 | This sequence change replaces glutamic acid, which is acidic and polar, with valine, which is neutral and non-polar, at codon 17 of the DNAJC21 protein (p.Glu17Val). This variant is present in population databases (no rsID available, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with DNAJC21-related conditions. ClinVar contains an entry for this variant (Variation ID: 2094655). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at