chr3-4516556-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP2PP3_Moderate
The NM_001378452.1(ITPR1):c.65C>T(p.Ser22Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000187 in 1,603,456 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S22S) has been classified as Likely benign.
Frequency
Consequence
NM_001378452.1 missense
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 |
---|---|---|---|---|---|---|---|
ITPR1 | NM_001378452.1 | c.65C>T | p.Ser22Leu | missense_variant | 3/62 | ENST00000649015.2 | |
ITPR1 | NM_001168272.2 | c.65C>T | p.Ser22Leu | missense_variant | 3/61 | ||
ITPR1 | NM_001099952.4 | c.65C>T | p.Ser22Leu | missense_variant | 3/59 | ||
ITPR1 | NM_002222.7 | c.65C>T | p.Ser22Leu | missense_variant | 3/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITPR1 | ENST00000649015.2 | c.65C>T | p.Ser22Leu | missense_variant | 3/62 | NM_001378452.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152138Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000413 AC: 1AN: 241938Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131580
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1451318Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 721956
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152138Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74312
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Sep 22, 2022 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at