rs1554770453
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_ModeratePM2PP5
The NM_052844.4(DYNC2I2):c.1567_1582del(p.Glu523ThrfsTer?) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,132 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. E523E) has been classified as Likely benign.
Frequency
Consequence
NM_052844.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYNC2I2 | NM_052844.4 | c.1567_1582del | p.Glu523ThrfsTer? | frameshift_variant | 9/9 | ENST00000372715.7 | |
DYNC2I2 | XM_011519179.3 | c.1483_1498del | p.Glu495ThrfsTer? | frameshift_variant | 10/10 | ||
DYNC2I2 | XM_047424057.1 | c.1567_1582del | p.Glu523ThrfsTer? | frameshift_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYNC2I2 | ENST00000372715.7 | c.1567_1582del | p.Glu523ThrfsTer? | frameshift_variant | 9/9 | 1 | NM_052844.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461132Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 726872
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Jeune thoracic dystrophy Pathogenic:2
Likely pathogenic, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | - | - - |
Pathogenic, no assertion criteria provided | research | Dan Cohn Lab, University Of California Los Angeles | Jun 01, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at