chr5-69282845-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_176816.5(CCDC125):āc.1420A>Gā(p.Ser474Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000044 in 1,613,986 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 (ā ).
Frequency
Consequence
NM_176816.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC125 | NM_176816.5 | c.1420A>G | p.Ser474Gly | missense_variant | 12/12 | ENST00000396496.7 | NP_789786.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC125 | ENST00000396496.7 | c.1420A>G | p.Ser474Gly | missense_variant | 12/12 | 5 | NM_176816.5 | ENSP00000379754 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000636 AC: 16AN: 251440Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135894
GnomAD4 exome AF: 0.0000417 AC: 61AN: 1461810Hom.: 0 Cov.: 32 AF XY: 0.0000578 AC XY: 42AN XY: 727210
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 23, 2023 | The c.1420A>G (p.S474G) alteration is located in exon 11 (coding exon 11) of the CCDC125 gene. This alteration results from a A to G substitution at nucleotide position 1420, causing the serine (S) at amino acid position 474 to be replaced by a glycine (G). 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