17-8735491-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_144681.3(CCDC42):c.613C>T(p.Arg205Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000153 in 1,614,074 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00016 ( 2 hom. )
Consequence
CCDC42
NM_144681.3 missense
NM_144681.3 missense
Scores
8
11
Clinical Significance
Conservation
PhyloP100: 4.50
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.3436581).
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC42 | NM_144681.3 | c.613C>T | p.Arg205Cys | missense_variant | 5/7 | ENST00000293845.8 | NP_653282.2 | |
CCDC42 | NM_001158261.2 | c.493-237C>T | intron_variant | NP_001151733.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC42 | ENST00000293845.8 | c.613C>T | p.Arg205Cys | missense_variant | 5/7 | 2 | NM_144681.3 | ENSP00000293845 | P1 | |
CCDC42 | ENST00000539522.2 | c.493-237C>T | intron_variant | 1 | ENSP00000444359 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152208Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000159 AC: 40AN: 250884Hom.: 1 AF XY: 0.000192 AC XY: 26AN XY: 135726
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GnomAD4 exome AF: 0.000158 AC: 231AN: 1461748Hom.: 2 Cov.: 33 AF XY: 0.000171 AC XY: 124AN XY: 727194
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GnomAD4 genome AF: 0.000105 AC: 16AN: 152326Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74480
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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 | Jun 10, 2024 | The c.613C>T (p.R205C) alteration is located in exon 5 (coding exon 5) of the CCDC42 gene. This alteration results from a C to T substitution at nucleotide position 613, causing the arginine (R) at amino acid position 205 to be replaced by a cysteine (C). 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
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
D
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