chr5-34929928-T-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001012339.3(DNAJC21):c.97+12T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000193 in 1,557,646 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 29)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
DNAJC21
NM_001012339.3 intron
NM_001012339.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.50
Genes affected
DNAJC21 (HGNC:27030): (DnaJ heat shock protein family (Hsp40) member C21) This gene encodes a member of the DNAJ heat shock protein 40 family of proteins that is characterized by two N-terminal tetratricopeptide repeat domains and a C-terminal DNAJ domain. This protein binds the precursor 45S ribosomal RNA and may be involved in early nuclear ribosomal RNA biogenesis and maturation of the 60S ribosomal subunit. Mutations in this gene result in Bone marrow failure syndrome 3. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
Variant 5-34929928-T-A is Benign according to our data. Variant chr5-34929928-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 2959934.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAJC21 | NM_001012339.3 | c.97+12T>A | intron_variant | ENST00000648817.1 | NP_001012339.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAJC21 | ENST00000648817.1 | c.97+12T>A | intron_variant | NM_001012339.3 | ENSP00000497410 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151698Hom.: 0 Cov.: 29
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GnomAD4 exome AF: 0.00000142 AC: 2AN: 1405948Hom.: 0 Cov.: 29 AF XY: 0.00000143 AC XY: 1AN XY: 698204
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GnomAD4 genome AF: 0.00000659 AC: 1AN: 151698Hom.: 0 Cov.: 29 AF XY: 0.0000135 AC XY: 1AN XY: 74106
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 23, 2023 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at