rs4252903

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

Scores

1
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0380
Variant links:
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]

Genome browser will be placed here

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
CCNINM_006835.3 linkuse as main transcriptc.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
CCNIENST00000237654.9 linkuse as main transcriptc.619G>A p.Val207Ile missense_variant 6/71 NM_006835.3 ENSP00000237654.4 Q14094-1
CCNIENST00000515468.1 linkuse as main transcriptc.87+741G>A intron_variant 3 ENSP00000425935.1 H0YA27
CCNIENST00000506614.1 linkuse as main transcriptn.*13G>A downstream_gene_variant 2

Frequencies

GnomAD3 genomes
AF:
0.00585
AC:
891
AN:
152178
Hom.:
9
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0202
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00223
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000103
Gnomad OTH
AF:
0.00574
GnomAD3 exomes
AF:
0.00165
AC:
414
AN:
251474
Hom.:
5
AF XY:
0.00115
AC XY:
156
AN XY:
135914
show subpopulations
Gnomad AFR exome
AF:
0.0229
Gnomad AMR exome
AF:
0.000925
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000527
Gnomad OTH exome
AF:
0.000651
GnomAD4 exome
AF:
0.000644
AC:
941
AN:
1461846
Hom.:
11
Cov.:
31
AF XY:
0.000567
AC XY:
412
AN XY:
727232
show subpopulations
Gnomad4 AFR exome
AF:
0.0227
Gnomad4 AMR exome
AF:
0.00101
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000369
Gnomad4 OTH exome
AF:
0.00152
GnomAD4 genome
AF:
0.00588
AC:
896
AN:
152296
Hom.:
9
Cov.:
33
AF XY:
0.00563
AC XY:
419
AN XY:
74470
show subpopulations
Gnomad4 AFR
AF:
0.0203
Gnomad4 AMR
AF:
0.00222
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000103
Gnomad4 OTH
AF:
0.00568
Alfa
AF:
0.00125
Hom.:
5
Bravo
AF:
0.00713
ESP6500AA
AF:
0.0225
AC:
99
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.00193
AC:
234
Asia WGS
AF:
0.000866
AC:
3
AN:
3478
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.082
BayesDel_addAF
Benign
-0.69
T
BayesDel_noAF
Benign
-0.74
CADD
Benign
13
DANN
Benign
0.36
DEOGEN2
Benign
0.085
T
Eigen
Benign
-0.61
Eigen_PC
Benign
-0.39
FATHMM_MKL
Benign
0.70
D
LIST_S2
Uncertain
0.89
D
MetaRNN
Benign
0.0080
T
MetaSVM
Benign
-0.98
T
MutationAssessor
Benign
-0.40
N
PrimateAI
Benign
0.37
T
PROVEAN
Benign
0.32
N
REVEL
Benign
0.040
Sift
Benign
1.0
T
Sift4G
Benign
1.0
T
Polyphen
0.0
B
Vest4
0.16
MVP
0.12
MPC
0.18
ClinPred
0.013
T
GERP RS
2.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.026
gMVP
0.16

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4252903; hg19: chr4-77976374; COSMIC: COSV99031667; COSMIC: COSV99031667; API