rs3936503

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_181698.4(CCNY):​c.-9+9703G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,986 control chromosomes in the GnomAD database, including 10,651 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 0.37 ( 10651 hom., cov: 31)

Consequence

CCNY
NM_181698.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.397
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCNYNM_181698.4 linkc.-9+9703G>A intron_variant Intron 3 of 11 NP_859049.2 Q8ND76-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCNYENST00000374706.5 linkc.-9+9703G>A intron_variant Intron 3 of 11 1 ENSP00000363838.1 Q8ND76-3
CCNYENST00000493157.6 linkc.-224+9703G>A intron_variant Intron 3 of 9 5 ENSP00000473625.1 R4GNF3
CCNYENST00000490012.6 linkc.-325+9703G>A intron_variant Intron 3 of 9 3 ENSP00000473487.1 R4GN48

Frequencies

GnomAD3 genomes
AF:
0.365
AC:
55465
AN:
151868
Hom.:
10633
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.486
Gnomad AMI
AF:
0.222
Gnomad AMR
AF:
0.303
Gnomad ASJ
AF:
0.409
Gnomad EAS
AF:
0.320
Gnomad SAS
AF:
0.324
Gnomad FIN
AF:
0.352
Gnomad MID
AF:
0.304
Gnomad NFE
AF:
0.315
Gnomad OTH
AF:
0.356
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.365
AC:
55537
AN:
151986
Hom.:
10651
Cov.:
31
AF XY:
0.365
AC XY:
27091
AN XY:
74282
show subpopulations
Gnomad4 AFR
AF:
0.486
Gnomad4 AMR
AF:
0.303
Gnomad4 ASJ
AF:
0.409
Gnomad4 EAS
AF:
0.320
Gnomad4 SAS
AF:
0.325
Gnomad4 FIN
AF:
0.352
Gnomad4 NFE
AF:
0.315
Gnomad4 OTH
AF:
0.364
Alfa
AF:
0.326
Hom.:
17465
Bravo
AF:
0.367
Asia WGS
AF:
0.351
AC:
1218
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.1
DANN
Benign
0.58

Splicing

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: rs3936503; hg19: chr10-35549257; API