rs764813110
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1PM2PP3_StrongPP5_Moderate
The NM_006736.6(DNAJB2):c.620-1G>A variant causes a splice acceptor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000038 in 1,579,948 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_006736.6 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJB2 | NM_006736.6 | c.620-1G>A | splice_acceptor_variant | ENST00000336576.10 | |||
DNAJB2 | NM_001039550.2 | c.620-1G>A | splice_acceptor_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJB2 | ENST00000336576.10 | c.620-1G>A | splice_acceptor_variant | 1 | NM_006736.6 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000856 AC: 2AN: 233754Hom.: 0 AF XY: 0.00000792 AC XY: 1AN XY: 126192
GnomAD4 exome AF: 0.00000280 AC: 4AN: 1427712Hom.: 0 Cov.: 31 AF XY: 0.00000142 AC XY: 1AN XY: 704842
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74382
ClinVar
Submissions by phenotype
Neuronopathy, distal hereditary motor, autosomal recessive 5 Pathogenic:1
Pathogenic, criteria provided, single submitter | research | Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine | Aug 18, 2015 | This variant is predicted deleterious according to ACMG guidelines and was identified in a homozygous state in an individual with peripheral axonal neuropathy. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at