rs1127354
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_StrongBA1
The NM_033453.4(ITPA):c.94C>A(p.Pro32Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0751 in 1,613,804 control chromosomes in the GnomAD database, including 5,117 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (★★★). Synonymous variant affecting the same amino acid position (i.e. P32P) has been classified as Likely benign.
Frequency
Consequence
NM_033453.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITPA | NM_033453.4 | c.94C>A | p.Pro32Thr | missense_variant | Exon 2 of 8 | ENST00000380113.8 | NP_258412.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0643 AC: 9779AN: 152138Hom.: 389 Cov.: 32
GnomAD3 exomes AF: 0.0752 AC: 18912AN: 251492Hom.: 971 AF XY: 0.0788 AC XY: 10708AN XY: 135920
GnomAD4 exome AF: 0.0762 AC: 111346AN: 1461548Hom.: 4730 Cov.: 32 AF XY: 0.0776 AC XY: 56419AN XY: 727094
GnomAD4 genome AF: 0.0642 AC: 9777AN: 152256Hom.: 387 Cov.: 32 AF XY: 0.0644 AC XY: 4793AN XY: 74438
ClinVar
Submissions by phenotype
Inosine triphosphatase deficiency Benign:1Other:1
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not specified Benign:1
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not provided Benign:1
This variant is associated with the following publications: (PMID: 17113761, 22060550, 22613675, 19914375, 24621321, 23528839, 19631656, 25525159, 22939045, 20173735, 21659334, 19682085, 23547827, 20547162, 20637204, 12384777, 27703193, 26394463, 30106365, 19579612) -
peginterferon alfa-2b and ribavirin response - Toxicity Other:1
PharmGKB Level of Evidence 2B: Variants in Level 2B clinical annotations are not in PharmGKB’s Tier 1 VIPs. These clinical annotations describe variant-drug combinations with a moderate level of evidence supporting the association. For example, the association may be found in multiple cohorts, but there may be a minority of studies that do not support the majority assertion. Level 2B clinical annotations must be supported by at least two independent publications. Drug-variant association: Toxicity
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at