GeneBe

NM_145012.6:c.154+52715A>G

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_145012.6(CCNY):​c.154+52715A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,138 control chromosomes in the GnomAD database, including 6,531 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 0.29 ( 6531 hom., cov: 32)

Consequence

CCNY
NM_145012.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0170

Publications

3 publications found
Variant links:
Genes affected
CCNY (HGNC:23354): (cyclin Y) Cyclins, such as CCNY, control cell division cycles and regulate cyclin-dependent kinases (e.g., CDC2; MIM 116940) (Li et al., 2009 [PubMed 18060517]).[supplied by OMIM, May 2009]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCNYNM_145012.6 linkc.154+52715A>G intron_variant Intron 1 of 9 ENST00000374704.8 NP_659449.3 Q8ND76-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCNYENST00000374704.8 linkc.154+52715A>G intron_variant Intron 1 of 9 1 NM_145012.6 ENSP00000363836.4 Q8ND76-1

Frequencies

GnomAD3 genomes
AF:
0.286
AC:
43502
AN:
152020
Hom.:
6522
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.203
Gnomad AMI
AF:
0.290
Gnomad AMR
AF:
0.347
Gnomad ASJ
AF:
0.376
Gnomad EAS
AF:
0.344
Gnomad SAS
AF:
0.317
Gnomad FIN
AF:
0.277
Gnomad MID
AF:
0.316
Gnomad NFE
AF:
0.312
Gnomad OTH
AF:
0.331
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.286
AC:
43526
AN:
152138
Hom.:
6531
Cov.:
32
AF XY:
0.285
AC XY:
21195
AN XY:
74374
show subpopulations
African (AFR)
AF:
0.203
AC:
8424
AN:
41510
American (AMR)
AF:
0.347
AC:
5308
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
0.376
AC:
1305
AN:
3470
East Asian (EAS)
AF:
0.344
AC:
1778
AN:
5168
South Asian (SAS)
AF:
0.318
AC:
1532
AN:
4824
European-Finnish (FIN)
AF:
0.277
AC:
2932
AN:
10576
Middle Eastern (MID)
AF:
0.313
AC:
92
AN:
294
European-Non Finnish (NFE)
AF:
0.312
AC:
21186
AN:
67978
Other (OTH)
AF:
0.334
AC:
706
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1578
3156
4735
6313
7891
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
440
880
1320
1760
2200
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.304
Hom.:
887
Bravo
AF:
0.292
Asia WGS
AF:
0.350
AC:
1217
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
9.2
DANN
Benign
0.66
PhyloP100
-0.017
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs11010188; hg19: chr10-35678850; API