rs4252903
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_001348140.2(CCNI):c.540G>A(p.Trp180*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00114 in 1,614,142 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0059 ( 9 hom., cov: 33)
Exomes 𝑓: 0.00064 ( 11 hom. )
Consequence
CCNI
NM_001348140.2 stop_gained
NM_001348140.2 stop_gained
Scores
1
17
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0380
Genes affected
CCNI (HGNC:1595): (cyclin I) The protein encoded by this gene belongs to the highly conserved cyclin family, whose members are characterized by a dramatic periodicity in protein abundance through the cell cycle. Cyclins function as regulators of CDK kinases. Different cyclins exhibit distinct expression and degradation patterns which contribute to the temporal coordination of each mitotic event. This cyclin shows the highest similarity with cyclin G. The transcript of this gene was found to be expressed constantly during cell cycle progression. [provided by RefSeq, Jan 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00588 (896/152296) while in subpopulation AFR AF= 0.0203 (842/41566). AF 95% confidence interval is 0.0191. There are 9 homozygotes in gnomad4. There are 419 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 896 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCNI | NM_006835.3 | c.619G>A | p.Val207Ile | missense_variant | 6/7 | ENST00000237654.9 | NP_006826.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCNI | ENST00000237654.9 | c.619G>A | p.Val207Ile | missense_variant | 6/7 | 1 | NM_006835.3 | ENSP00000237654.4 | ||
CCNI | ENST00000515468.1 | c.87+741G>A | intron_variant | 3 | ENSP00000425935.1 | |||||
CCNI | ENST00000506614.1 | n.*13G>A | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00585 AC: 891AN: 152178Hom.: 9 Cov.: 33
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GnomAD3 exomes AF: 0.00165 AC: 414AN: 251474Hom.: 5 AF XY: 0.00115 AC XY: 156AN XY: 135914
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GnomAD4 exome AF: 0.000644 AC: 941AN: 1461846Hom.: 11 Cov.: 31 AF XY: 0.000567 AC XY: 412AN XY: 727232
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GnomAD4 genome AF: 0.00588 AC: 896AN: 152296Hom.: 9 Cov.: 33 AF XY: 0.00563 AC XY: 419AN XY: 74470
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
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