rs9469559
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002224.4(ITPR3):c.5456G>A(p.Arg1819His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000666 in 1,612,894 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_002224.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITPR3 | ENST00000605930.3 | c.5456G>A | p.Arg1819His | missense_variant | Exon 40 of 58 | 1 | NM_002224.4 | ENSP00000475177.1 | ||
ITPR3 | ENST00000374316.9 | c.5456G>A | p.Arg1819His | missense_variant | Exon 41 of 59 | 5 | ENSP00000363435.4 |
Frequencies
GnomAD3 genomes AF: 0.00331 AC: 504AN: 152192Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.000939 AC: 232AN: 247072Hom.: 3 AF XY: 0.000798 AC XY: 107AN XY: 134152
GnomAD4 exome AF: 0.000390 AC: 569AN: 1460584Hom.: 7 Cov.: 39 AF XY: 0.000354 AC XY: 257AN XY: 726580
GnomAD4 genome AF: 0.00332 AC: 505AN: 152310Hom.: 4 Cov.: 33 AF XY: 0.00341 AC XY: 254AN XY: 74468
ClinVar
Submissions by phenotype
ITPR3-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at