rs139406455
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006736.6(DNAJB2):c.298G>A(p.Glu100Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000343 in 1,614,184 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E100G) has been classified as Uncertain significance.
Frequency
Consequence
NM_006736.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJB2 | NM_006736.6 | c.298G>A | p.Glu100Lys | missense_variant | 5/9 | ENST00000336576.10 | |
DNAJB2 | NM_001039550.2 | c.298G>A | p.Glu100Lys | missense_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJB2 | ENST00000336576.10 | c.298G>A | p.Glu100Lys | missense_variant | 5/9 | 1 | NM_006736.6 |
Frequencies
GnomAD3 genomes ? AF: 0.00166 AC: 252AN: 152188Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.000382 AC: 96AN: 251464Hom.: 2 AF XY: 0.000331 AC XY: 45AN XY: 135914
GnomAD4 exome AF: 0.000206 AC: 301AN: 1461878Hom.: 2 Cov.: 32 AF XY: 0.000195 AC XY: 142AN XY: 727240
GnomAD4 genome ? AF: 0.00165 AC: 252AN: 152306Hom.: 4 Cov.: 32 AF XY: 0.00169 AC XY: 126AN XY: 74480
ClinVar
Submissions by phenotype
Charcot-Marie-Tooth disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Molecular Genetics Laboratory, London Health Sciences Centre | - | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 25, 2020 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 13, 2020 | - - |
Neuronopathy, distal hereditary motor, autosomal recessive 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at