6-75922166-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001563.4(IMPG1):c.2317G>A(p.Val773Ile) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001563.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IMPG1 | NM_001563.4 | c.2317G>A | p.Val773Ile | missense_variant, splice_region_variant | 17/17 | ENST00000369950.8 | |
IMPG1 | NM_001282368.2 | c.2083G>A | p.Val695Ile | missense_variant, splice_region_variant | 16/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IMPG1 | ENST00000369950.8 | c.2317G>A | p.Val773Ile | missense_variant, splice_region_variant | 17/17 | 1 | NM_001563.4 | P2 | |
IMPG1 | ENST00000611179.4 | c.2083G>A | p.Val695Ile | missense_variant, splice_region_variant | 16/16 | 5 | A2 | ||
IMPG1 | ENST00000369952.3 | c.400G>A | p.Val134Ile | missense_variant, splice_region_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000529 AC: 1AN: 189208Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 100830
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000179 AC: 2AN: 1116162Hom.: 0 Cov.: 15 AF XY: 0.00000177 AC XY: 1AN XY: 565716
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152092Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74292
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 22, 2023 | This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 773 of the IMPG1 protein (p.Val773Ile). This variant is present in population databases (no rsID available, gnomAD 0.004%). 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: 2001168). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The isoleucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at