rs587777224
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5
The NM_145261.4(DNAJC19):c.300del(p.Ala101ProfsTer10) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000342 in 1,608,072 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. A100A) has been classified as Likely benign.
Frequency
Consequence
NM_145261.4 frameshift
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJC19 | NM_145261.4 | c.300del | p.Ala101ProfsTer10 | frameshift_variant | 6/6 | ENST00000382564.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJC19 | ENST00000382564.8 | c.300del | p.Ala101ProfsTer10 | frameshift_variant | 6/6 | 1 | NM_145261.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000724 AC: 11AN: 151972Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000813 AC: 20AN: 246058Hom.: 0 AF XY: 0.0000751 AC XY: 10AN XY: 133158
GnomAD4 exome AF: 0.0000302 AC: 44AN: 1456100Hom.: 0 Cov.: 29 AF XY: 0.0000262 AC XY: 19AN XY: 724412
GnomAD4 genome ? AF: 0.0000724 AC: 11AN: 151972Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74244
ClinVar
Submissions by phenotype
3-methylglutaconic aciduria type 5 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 2012 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at