12-26427995-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_002223.4(ITPR2):c.6863G>A(p.Arg2288Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,612,378 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002223.4 missense
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITPR2 | NM_002223.4 | c.6863G>A | p.Arg2288Gln | missense_variant | 49/57 | ENST00000381340.8 | NP_002214.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITPR2 | ENST00000381340.8 | c.6863G>A | p.Arg2288Gln | missense_variant | 49/57 | 1 | NM_002223.4 | ENSP00000370744.3 | ||
ITPR2 | ENST00000451599.6 | n.*1382G>A | non_coding_transcript_exon_variant | 12/18 | 1 | ENSP00000408287.2 | ||||
ITPR2 | ENST00000451599.6 | n.*1382G>A | 3_prime_UTR_variant | 12/18 | 1 | ENSP00000408287.2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151850Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 247912Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134554
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460528Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 726546
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151850Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74150
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 28, 2024 | The c.6863G>A (p.R2288Q) alteration is located in exon 49 (coding exon 49) of the ITPR2 gene. This alteration results from a G to A substitution at nucleotide position 6863, causing the arginine (R) at amino acid position 2288 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at