rs760430736
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015891.3(CDC40):āc.659C>Gā(p.Thr220Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000000701 in 1,425,632 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes š: 7.0e-7 ( 0 hom. )
Consequence
CDC40
NM_015891.3 missense
NM_015891.3 missense
Scores
2
8
9
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.48
Genes affected
CDC40 (HGNC:17350): (cell division cycle 40) Pre-mRNA splicing occurs in two sequential transesterification steps. The protein encoded by this gene is found to be essential for the catalytic step II in pre-mRNA splicing process. It is found in the spliceosome, and contains seven WD repeats, which function in protein-protein interactions. This protein has a sequence similarity to yeast Prp17 protein, which functions in two different cellular processes: pre-mRNA splicing and cell cycle progression. It suggests that this protein may play a role in cell cycle progression. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDC40 | ENST00000307731.2 | c.659C>G | p.Thr220Arg | missense_variant | Exon 6 of 15 | 1 | NM_015891.3 | ENSP00000304370.1 | ||
CDC40 | ENST00000368932.5 | c.659C>G | p.Thr220Arg | missense_variant | Exon 7 of 16 | 5 | ENSP00000357928.1 | |||
CDC40 | ENST00000368930.5 | c.659C>G | p.Thr220Arg | missense_variant | Exon 6 of 15 | 2 | ENSP00000357926.1 | |||
CDC40 | ENST00000606893.5 | n.760C>G | non_coding_transcript_exon_variant | Exon 7 of 15 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000444 AC: 1AN: 224988Hom.: 0 AF XY: 0.00000818 AC XY: 1AN XY: 122264
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GnomAD4 exome AF: 7.01e-7 AC: 1AN: 1425632Hom.: 0 Cov.: 28 AF XY: 0.00000141 AC XY: 1AN XY: 708956
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
.;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
P;P;.
Vest4
MutPred
Loss of sheet (P = 7e-04);Loss of sheet (P = 7e-04);Loss of sheet (P = 7e-04);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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