16-19114607-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001034841.4(ITPRIPL2):c.146C>T(p.Pro49Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000379 in 1,583,966 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_001034841.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITPRIPL2 | ENST00000381440.5 | c.146C>T | p.Pro49Leu | missense_variant | Exon 1 of 1 | 6 | NM_001034841.4 | ENSP00000370849.3 | ||
ENSG00000261427 | ENST00000564808.6 | n.124-34C>T | intron_variant | Intron 1 of 5 | 4 | |||||
ITPRIPL2 | ENST00000566735.1 | n.194-34C>T | intron_variant | Intron 1 of 1 | 2 | |||||
ENSG00000261427 | ENST00000568526.1 | n.67-34C>T | intron_variant | Intron 1 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000431 AC: 9AN: 208878Hom.: 0 AF XY: 0.0000525 AC XY: 6AN XY: 114358
GnomAD4 exome AF: 0.0000391 AC: 56AN: 1431770Hom.: 0 Cov.: 31 AF XY: 0.0000479 AC XY: 34AN XY: 710524
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.146C>T (p.P49L) alteration is located in exon 1 (coding exon 1) of the ITPRIPL2 gene. This alteration results from a C to T substitution at nucleotide position 146, causing the proline (P) at amino acid position 49 to be replaced by a leucine (L). 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