chr7-31553113-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001257967.3(ITPRID1):c.89C>T(p.Ala30Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 1,601,312 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 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. A30T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001257967.3 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 |
---|---|---|---|---|---|---|---|
ITPRID1 | NM_001257967.3 | c.89C>T | p.Ala30Val | missense_variant | 3/15 | ENST00000615280.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITPRID1 | ENST00000615280.5 | c.89C>T | p.Ala30Val | missense_variant | 3/15 | 2 | NM_001257967.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000877 AC: 20AN: 228168Hom.: 0 AF XY: 0.0000899 AC XY: 11AN XY: 122352
GnomAD4 exome AF: 0.000123 AC: 178AN: 1449164Hom.: 0 Cov.: 30 AF XY: 0.000133 AC XY: 96AN XY: 719448
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152148Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2021 | The c.89C>T (p.A30V) alteration is located in exon 2 (coding exon 1) of the CCDC129 gene. This alteration results from a C to T substitution at nucleotide position 89, causing the alanine (A) at amino acid position 30 to be replaced by a valine (V). 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