5-69307992-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_176816.5(CCDC125):c.490G>A(p.Val164Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00019 in 1,613,936 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_176816.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC125 | NM_176816.5 | c.490G>A | p.Val164Met | missense_variant | 5/12 | ENST00000396496.7 | NP_789786.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC125 | ENST00000396496.7 | c.490G>A | p.Val164Met | missense_variant | 5/12 | 5 | NM_176816.5 | ENSP00000379754 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000994 AC: 25AN: 251404Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135884
GnomAD4 exome AF: 0.000194 AC: 284AN: 1461728Hom.: 0 Cov.: 29 AF XY: 0.000194 AC XY: 141AN XY: 727192
GnomAD4 genome AF: 0.000151 AC: 23AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2022 | The c.490G>A (p.V164M) alteration is located in exon 4 (coding exon 4) of the CCDC125 gene. This alteration results from a G to A substitution at nucleotide position 490, causing the valine (V) at amino acid position 164 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