chr10-104315361-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001272013.2(ITPRIP):c.691C>T(p.Arg231Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000355 in 1,409,424 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R231H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001272013.2 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 |
---|---|---|---|---|---|---|---|
ITPRIP | NM_001272013.2 | c.691C>T | p.Arg231Cys | missense_variant | 2/2 | ENST00000337478.3 | |
ITPRIP | NM_001272012.2 | c.691C>T | p.Arg231Cys | missense_variant | 2/2 | ||
ITPRIP | NM_033397.4 | c.691C>T | p.Arg231Cys | missense_variant | 3/3 | ||
ITPRIP | XM_005270257.3 | c.706C>T | p.Arg236Cys | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITPRIP | ENST00000337478.3 | c.691C>T | p.Arg231Cys | missense_variant | 2/2 | 1 | NM_001272013.2 | P1 | |
ITPRIP | ENST00000278071.6 | c.691C>T | p.Arg231Cys | missense_variant | 3/3 | 1 | P1 | ||
ITPRIP | ENST00000358187.2 | c.691C>T | p.Arg231Cys | missense_variant | 2/2 | 2 | P1 | ||
ITPRIP | ENST00000647721.1 | c.691C>T | p.Arg231Cys | missense_variant | 3/3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000473 AC: 1AN: 211268Hom.: 0 AF XY: 0.00000894 AC XY: 1AN XY: 111904
GnomAD4 exome AF: 0.00000355 AC: 5AN: 1409424Hom.: 0 Cov.: 34 AF XY: 0.00000432 AC XY: 3AN XY: 693848
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.691C>T (p.R231C) alteration is located in exon 3 (coding exon 1) of the ITPRIP gene. This alteration results from a C to T substitution at nucleotide position 691, causing the arginine (R) at amino acid position 231 to be replaced by a cysteine (C). 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