chr1-226735804-G-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002221.4(ITPKB):c.1655C>A(p.Pro552Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.95 in 1,607,554 control chromosomes in the GnomAD database, including 726,057 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 Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002221.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITPKB | NM_002221.4 | c.1655C>A | p.Pro552Gln | missense_variant | 2/8 | ENST00000429204.6 | |
ITPKB | NM_001388404.1 | c.1655C>A | p.Pro552Gln | missense_variant | 2/3 | ||
ITPKB | XM_017001211.3 | c.1655C>A | p.Pro552Gln | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITPKB | ENST00000429204.6 | c.1655C>A | p.Pro552Gln | missense_variant | 2/8 | 5 | NM_002221.4 | P1 | |
ITPKB | ENST00000272117.8 | c.1655C>A | p.Pro552Gln | missense_variant | 2/8 | 1 | P1 | ||
ITPKB | ENST00000366784.1 | c.1655C>A | p.Pro552Gln | missense_variant | 2/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.961 AC: 146198AN: 152142Hom.: 70276 Cov.: 31
GnomAD3 exomes AF: 0.964 AC: 241547AN: 250586Hom.: 116476 AF XY: 0.964 AC XY: 130582AN XY: 135442
GnomAD4 exome AF: 0.949 AC: 1381154AN: 1455294Hom.: 655722 Cov.: 55 AF XY: 0.950 AC XY: 686420AN XY: 722484
GnomAD4 genome ? AF: 0.961 AC: 146316AN: 152260Hom.: 70335 Cov.: 31 AF XY: 0.963 AC XY: 71688AN XY: 74430
ClinVar
Submissions by phenotype
Myeloproliferative neoplasm, unclassifiable Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Dept. of Cytogenetics, ICMR- National Institute of Immunohaematology | Aug 25, 2022 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 99% of patients studied by a panel of primary immunodeficiencies. Number of patients: 94. Only high quality variants are reported. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at