chr6-7575487-AG-A
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1PM2PP3_ModeratePP5_Moderate
The NM_004415.4(DSP):c.2630+1del variant causes a frameshift, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. R877R) has been classified as Benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_004415.4 frameshift, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DSP | NM_004415.4 | c.2630+1del | frameshift_variant, splice_region_variant | 18/24 | ENST00000379802.8 | ||
DSP | NM_001319034.2 | c.2630+1del | frameshift_variant, splice_region_variant | 18/24 | |||
DSP | NM_001008844.3 | c.2630+1del | frameshift_variant, splice_region_variant | 18/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DSP | ENST00000379802.8 | c.2630+1del | frameshift_variant, splice_region_variant | 18/24 | 1 | NM_004415.4 | P2 | ||
DSP | ENST00000418664.2 | c.2630+1del | frameshift_variant, splice_region_variant | 18/24 | 1 | A2 | |||
DSP | ENST00000710359.1 | c.2630+1del | frameshift_variant, splice_region_variant | 18/24 | A2 | ||||
DSP | ENST00000684395.1 | n.1272del | non_coding_transcript_exon_variant | 5/5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 34
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute | Aug 29, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at