NM_003024.3:c.147dupT
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 8P and 5B. PVS1BS1_SupportingBS2
The NM_003024.3(ITSN1):c.147dupT(p.Gln50SerfsTer17) variant causes a frameshift change. The variant allele was found at a frequency of 0.000189 in 1,350,280 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_003024.3 frameshift
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITSN1 | ENST00000381318.8 | c.147dupT | p.Gln50SerfsTer17 | frameshift_variant | Exon 4 of 40 | 1 | NM_003024.3 | ENSP00000370719.3 | ||
ENSG00000249209 | ENST00000429238.2 | c.442-136424dupA | intron_variant | Intron 6 of 7 | 5 | ENSP00000394107.2 |
Frequencies
GnomAD3 genomes AF: 0.00000693 AC: 1AN: 144242Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.000189 AC: 255AN: 1350280Hom.: 0 Cov.: 35 AF XY: 0.000213 AC XY: 143AN XY: 670366
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000693 AC: 1AN: 144242Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 69932
ClinVar
Submissions by phenotype
not provided Uncertain:1
Reported in a study evaluating associations between loss-of-function variants in the ITSN1 gene and Parkinson's disease; however, specific clinical information was not provided (PMID: 39147844); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 39147844) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at