1-65398860-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001256864.2(DNAJC6):āc.2086T>Gā(p.Trp696Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,780 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. W696R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001256864.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAJC6 | NM_001256864.2 | c.2086T>G | p.Trp696Gly | missense_variant | 14/19 | ENST00000371069.5 | NP_001243793.1 | |
DNAJC6 | NM_014787.4 | c.1915T>G | p.Trp639Gly | missense_variant | 14/19 | NP_055602.1 | ||
DNAJC6 | NM_001256865.2 | c.1876T>G | p.Trp626Gly | missense_variant | 15/20 | NP_001243794.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAJC6 | ENST00000371069.5 | c.2086T>G | p.Trp696Gly | missense_variant | 14/19 | 1 | NM_001256864.2 | ENSP00000360108.4 | ||
DNAJC6 | ENST00000395325.7 | c.1915T>G | p.Trp639Gly | missense_variant | 14/19 | 1 | ENSP00000378735.3 | |||
DNAJC6 | ENST00000263441.11 | c.1876T>G | p.Trp626Gly | missense_variant | 15/20 | 2 | ENSP00000263441.7 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461780Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727196
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Dec 17, 2019 | Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge; In silico analysis, which includes splice predictors and evolutionary conservation, suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.