chr6-75922144-TC-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PVS1_Moderate
The NM_001563.4(IMPG1):c.2338delG(p.Glu780AsnfsTer3) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000135 in 1,403,200 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001563.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IMPG1 | NM_001563.4 | c.2338delG | p.Glu780AsnfsTer3 | frameshift_variant | Exon 17 of 17 | ENST00000369950.8 | NP_001554.2 | |
IMPG1 | NM_001282368.2 | c.2104delG | p.Glu702AsnfsTer3 | frameshift_variant | Exon 16 of 16 | NP_001269297.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IMPG1 | ENST00000369950.8 | c.2338delG | p.Glu780AsnfsTer3 | frameshift_variant | Exon 17 of 17 | 1 | NM_001563.4 | ENSP00000358966.3 | ||
IMPG1 | ENST00000611179.4 | c.2104delG | p.Glu702AsnfsTer3 | frameshift_variant | Exon 16 of 16 | 5 | ENSP00000481913.1 | |||
IMPG1 | ENST00000369952.3 | c.421delG | p.Glu141AsnfsTer3 | frameshift_variant | Exon 4 of 4 | 3 | ENSP00000358968.3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000195 AC: 4AN: 204932Hom.: 0 AF XY: 0.0000183 AC XY: 2AN XY: 109442
GnomAD4 exome AF: 0.0000136 AC: 17AN: 1250996Hom.: 0 Cov.: 18 AF XY: 0.0000191 AC XY: 12AN XY: 628578
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74358
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change creates a premature translational stop signal (p.Glu780Asnfs*3) in the IMPG1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 18 amino acid(s) of the IMPG1 protein. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant is present in population databases (no rsID available, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with IMPG1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1010628). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at