rs11645060
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005147.6(DNAJA3):c.430-315G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0495 in 439,494 control chromosomes in the GnomAD database, including 692 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.043 ( 198 hom., cov: 31)
Exomes 𝑓: 0.053 ( 494 hom. )
Consequence
DNAJA3
NM_005147.6 intron
NM_005147.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.00600
Genes affected
DNAJA3 (HGNC:11808): (DnaJ heat shock protein family (Hsp40) member A3) This gene encodes a member of the DNAJ/Hsp40 protein family. DNAJ/Hsp40 proteins stimulate the ATPase activity of Hsp70 chaperones and play critical roles in protein folding, degradation, and multimeric complex assembly. The encoded protein is localized to mitochondria and mediates several cellular processes including proliferation, survival and apoptotic signal transduction. The encoded protein also plays a critical role in tumor suppression through interactions with oncogenic proteins including ErbB2 and the p53 tumor suppressor protein. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0621 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJA3 | NM_005147.6 | c.430-315G>A | intron_variant | ENST00000262375.11 | |||
DNAJA3 | NM_001135110.3 | c.430-315G>A | intron_variant | ||||
DNAJA3 | NM_001286516.2 | c.102-446G>A | intron_variant | ||||
DNAJA3 | XM_047434875.1 | c.430-315G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJA3 | ENST00000262375.11 | c.430-315G>A | intron_variant | 1 | NM_005147.6 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0426 AC: 6481AN: 152218Hom.: 198 Cov.: 31
GnomAD3 genomes
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GnomAD4 exome AF: 0.0533 AC: 15292AN: 287158Hom.: 494 Cov.: 0 AF XY: 0.0539 AC XY: 7982AN XY: 148106
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GnomAD4 genome ? AF: 0.0425 AC: 6479AN: 152336Hom.: 198 Cov.: 31 AF XY: 0.0425 AC XY: 3164AN XY: 74496
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at