GeneBe

NM_145012.6:c.154+43193G>A

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+43193G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0818 in 152,242 control chromosomes in the GnomAD database, including 938 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 0.082 ( 938 hom., cov: 32)

Consequence

CCNY
NM_145012.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.160

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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCNYNM_145012.6 linkc.154+43193G>A 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+43193G>A intron_variant Intron 1 of 9 1 NM_145012.6 ENSP00000363836.4 Q8ND76-1

Frequencies

GnomAD3 genomes
AF:
0.0816
AC:
12409
AN:
152124
Hom.:
929
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.200
Gnomad AMI
AF:
0.0504
Gnomad AMR
AF:
0.0607
Gnomad ASJ
AF:
0.0691
Gnomad EAS
AF:
0.0558
Gnomad SAS
AF:
0.0168
Gnomad FIN
AF:
0.0148
Gnomad MID
AF:
0.0601
Gnomad NFE
AF:
0.0329
Gnomad OTH
AF:
0.0703
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0818
AC:
12451
AN:
152242
Hom.:
938
Cov.:
32
AF XY:
0.0804
AC XY:
5983
AN XY:
74452
show subpopulations
African (AFR)
AF:
0.200
AC:
8310
AN:
41514
American (AMR)
AF:
0.0607
AC:
928
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
0.0691
AC:
240
AN:
3472
East Asian (EAS)
AF:
0.0557
AC:
289
AN:
5184
South Asian (SAS)
AF:
0.0168
AC:
81
AN:
4824
European-Finnish (FIN)
AF:
0.0148
AC:
157
AN:
10606
Middle Eastern (MID)
AF:
0.0578
AC:
17
AN:
294
European-Non Finnish (NFE)
AF:
0.0329
AC:
2236
AN:
68026
Other (OTH)
AF:
0.0696
AC:
147
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
529
1058
1587
2116
2645
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
128
256
384
512
640
<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:
0.0657
Hom.:
87
Bravo
AF:
0.0900
Asia WGS
AF:
0.0400
AC:
140
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.19
DANN
Benign
0.57
PhyloP100
-0.16
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: rs2504353; hg19: chr10-35669328; API