rs3936503
Variant names:
Your query was ambiguous. Multiple possible variants found:
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
NM_181698.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.397
Genes affected
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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCNY | ENST00000374706.5 | c.-9+9703G>A | intron_variant | Intron 3 of 11 | 1 | ENSP00000363838.1 | ||||
CCNY | ENST00000493157.6 | c.-224+9703G>A | intron_variant | Intron 3 of 9 | 5 | ENSP00000473625.1 | ||||
CCNY | ENST00000490012.6 | c.-325+9703G>A | intron_variant | Intron 3 of 9 | 3 | ENSP00000473487.1 |
Frequencies
GnomAD3 genomes AF: 0.365 AC: 55465AN: 151868Hom.: 10633 Cov.: 31
GnomAD3 genomes
AF:
AC:
55465
AN:
151868
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.365 AC: 55537AN: 151986Hom.: 10651 Cov.: 31 AF XY: 0.365 AC XY: 27091AN XY: 74282
GnomAD4 genome
AF:
AC:
55537
AN:
151986
Hom.:
Cov.:
31
AF XY:
AC XY:
27091
AN XY:
74282
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1218
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at