19-40717296-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_025194.3(ITPKC):c.161A>C(p.Glu54Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000626 in 1,484,812 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_025194.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITPKC | NM_025194.3 | c.161A>C | p.Glu54Ala | missense_variant | 1/7 | ENST00000263370.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITPKC | ENST00000263370.3 | c.161A>C | p.Glu54Ala | missense_variant | 1/7 | 1 | NM_025194.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151218Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000188 AC: 2AN: 106212Hom.: 0 AF XY: 0.0000167 AC XY: 1AN XY: 59786
GnomAD4 exome AF: 0.0000675 AC: 90AN: 1333594Hom.: 0 Cov.: 31 AF XY: 0.0000640 AC XY: 42AN XY: 656046
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151218Hom.: 0 Cov.: 31 AF XY: 0.0000271 AC XY: 2AN XY: 73878
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2022 | The c.161A>C (p.E54A) alteration is located in exon 1 (coding exon 1) of the ITPKC gene. This alteration results from a A to C substitution at nucleotide position 161, causing the glutamic acid (E) at amino acid position 54 to be replaced by an alanine (A). 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