chr1-226735813-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBS2_Supporting
The NM_002221.4(ITPKB):āc.1646C>Gā(p.Pro549Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000286 in 1,608,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_002221.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITPKB | NM_002221.4 | c.1646C>G | p.Pro549Arg | missense_variant | 2/8 | ENST00000429204.6 | |
ITPKB | NM_001388404.1 | c.1646C>G | p.Pro549Arg | missense_variant | 2/3 | ||
ITPKB | XM_017001211.3 | c.1646C>G | p.Pro549Arg | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITPKB | ENST00000429204.6 | c.1646C>G | p.Pro549Arg | missense_variant | 2/8 | 5 | NM_002221.4 | P1 | |
ITPKB | ENST00000272117.8 | c.1646C>G | p.Pro549Arg | missense_variant | 2/8 | 1 | P1 | ||
ITPKB | ENST00000366784.1 | c.1646C>G | p.Pro549Arg | missense_variant | 2/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152088Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000479 AC: 12AN: 250542Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135466
GnomAD4 exome AF: 0.0000288 AC: 42AN: 1456080Hom.: 0 Cov.: 40 AF XY: 0.0000332 AC XY: 24AN XY: 723074
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152088Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74288
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2023 | The c.1646C>G (p.P549R) alteration is located in exon 2 (coding exon 1) of the ITPKB gene. This alteration results from a C to G substitution at nucleotide position 1646, causing the proline (P) at amino acid position 549 to be replaced by an arginine (R). 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