chr10-104315360-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001272013.2(ITPRIP):c.692G>A(p.Arg231His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000532 in 1,560,626 control chromosomes in the GnomAD database, including 2 homozygotes. 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. R231C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001272013.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITPRIP | NM_001272013.2 | c.692G>A | p.Arg231His | missense_variant | 2/2 | ENST00000337478.3 | |
ITPRIP | NM_001272012.2 | c.692G>A | p.Arg231His | missense_variant | 2/2 | ||
ITPRIP | NM_033397.4 | c.692G>A | p.Arg231His | missense_variant | 3/3 | ||
ITPRIP | XM_005270257.3 | c.707G>A | p.Arg236His | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITPRIP | ENST00000337478.3 | c.692G>A | p.Arg231His | missense_variant | 2/2 | 1 | NM_001272013.2 | P1 | |
ITPRIP | ENST00000278071.6 | c.692G>A | p.Arg231His | missense_variant | 3/3 | 1 | P1 | ||
ITPRIP | ENST00000358187.2 | c.692G>A | p.Arg231His | missense_variant | 2/2 | 2 | P1 | ||
ITPRIP | ENST00000647721.1 | c.692G>A | p.Arg231His | missense_variant | 3/3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000713 AC: 15AN: 210522Hom.: 0 AF XY: 0.0000628 AC XY: 7AN XY: 111500
GnomAD4 exome AF: 0.0000525 AC: 74AN: 1408426Hom.: 2 Cov.: 33 AF XY: 0.0000606 AC XY: 42AN XY: 693260
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.692G>A (p.R231H) alteration is located in exon 3 (coding exon 1) of the ITPRIP gene. This alteration results from a G to A substitution at nucleotide position 692, causing the arginine (R) at amino acid position 231 to be replaced by a histidine (H). 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