chr5-69292269-G-C
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_176816.5(CCDC125):āc.1018C>Gā(p.Gln340Glu) variant causes a missense change. The variant allele was found at a frequency of 0.000107 in 1,613,500 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00015 ( 0 hom., cov: 32)
Exomes š: 0.00010 ( 1 hom. )
Consequence
CCDC125
NM_176816.5 missense
NM_176816.5 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: 4.16
Genes affected
CCDC125 (HGNC:28924): (coiled-coil domain containing 125) Enables identical protein binding activity. Involved in activation of GTPase activity; negative regulation of Rho protein signal transduction; and negative regulation of cell motility. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.071434855).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC125 | NM_176816.5 | c.1018C>G | p.Gln340Glu | missense_variant | 10/12 | ENST00000396496.7 | NP_789786.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC125 | ENST00000396496.7 | c.1018C>G | p.Gln340Glu | missense_variant | 10/12 | 5 | NM_176816.5 | ENSP00000379754 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152138Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000995 AC: 25AN: 251200Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135786
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GnomAD4 exome AF: 0.000103 AC: 150AN: 1461244Hom.: 1 Cov.: 31 AF XY: 0.000113 AC XY: 82AN XY: 726964
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GnomAD4 genome AF: 0.000151 AC: 23AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74440
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2021 | The c.1018C>G (p.Q340E) alteration is located in exon 9 (coding exon 9) of the CCDC125 gene. This alteration results from a C to G substitution at nucleotide position 1018, causing the glutamine (Q) at amino acid position 340 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.
MutationTaster
Benign
D;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
P;P;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at