chr7-31577976-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001257967.3(ITPRID1):c.712G>A(p.Val238Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,644 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 (★).
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.712G>A | p.Val238Met | missense_variant | 9/15 | ENST00000615280.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITPRID1 | ENST00000615280.5 | c.712G>A | p.Val238Met | missense_variant | 9/15 | 2 | NM_001257967.3 | P2 | |
ITPRID1 | ENST00000407970.7 | c.712G>A | p.Val238Met | missense_variant | 8/14 | 1 | P2 | ||
ITPRID1 | ENST00000409210.1 | c.436G>A | p.Val146Met | missense_variant | 6/13 | 2 | A2 | ||
ITPRID1 | ENST00000319386.7 | c.712G>A | p.Val238Met | missense_variant | 8/14 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152150Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461494Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727022
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.712G>A (p.V238M) alteration is located in exon 8 (coding exon 7) of the CCDC129 gene. This alteration results from a G to A substitution at nucleotide position 712, causing the valine (V) at amino acid position 238 to be replaced by a methionine (M). 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