chr20-33386589-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016408.4(CDK5RAP1):c.755+734C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 151,892 control chromosomes in the GnomAD database, including 35,547 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 0.68 ( 35547 hom., cov: 31)
Consequence
CDK5RAP1
NM_016408.4 intron
NM_016408.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.163
Publications
7 publications found
Genes affected
CDK5RAP1 (HGNC:15880): (CDK5 regulatory subunit associated protein 1) This gene encodes a regulator of cyclin-dependent kinase 5 activity. This protein has also been reported to modify RNA by adding a methylthio-group and may thus have a dual function as an RNA methylthiotransferase and as an inhibitor of cyclin-dependent kinase 5 activity. Alternative splicing results in multiple transcript variants that encode different isoforms. [provided by RefSeq, May 2013]
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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=-0.99).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDK5RAP1 | NM_016408.4 | c.755+734C>T | intron_variant | Intron 6 of 13 | ENST00000346416.7 | NP_057492.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.682 AC: 103578AN: 151774Hom.: 35497 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
103578
AN:
151774
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: 0.683 AC: 103683AN: 151892Hom.: 35547 Cov.: 31 AF XY: 0.680 AC XY: 50430AN XY: 74206 show subpopulations
GnomAD4 genome
AF:
AC:
103683
AN:
151892
Hom.:
Cov.:
31
AF XY:
AC XY:
50430
AN XY:
74206
show subpopulations
African (AFR)
AF:
AC:
28533
AN:
41434
American (AMR)
AF:
AC:
11323
AN:
15244
Ashkenazi Jewish (ASJ)
AF:
AC:
2395
AN:
3468
East Asian (EAS)
AF:
AC:
3251
AN:
5156
South Asian (SAS)
AF:
AC:
3341
AN:
4810
European-Finnish (FIN)
AF:
AC:
6163
AN:
10526
Middle Eastern (MID)
AF:
AC:
202
AN:
294
European-Non Finnish (NFE)
AF:
AC:
46394
AN:
67950
Other (OTH)
AF:
AC:
1448
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1658
3315
4973
6630
8288
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
808
1616
2424
3232
4040
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2434
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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