rs10946398
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017774.3(CDKAL1):c.371+11426A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,990 control chromosomes in the GnomAD database, including 13,060 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: 𝑓 0.40 ( 13060 hom., cov: 32)
Consequence
CDKAL1
NM_017774.3 intron
NM_017774.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.132
Genes affected
CDKAL1 (HGNC:21050): (CDK5 regulatory subunit associated protein 1 like 1) The protein encoded by this gene is a member of the methylthiotransferase family. The function of this gene is not known. Genome-wide association studies have linked single nucleotide polymorphisms in an intron of this gene with susceptibilty to type 2 diabetes. [provided by RefSeq, May 2010]
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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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.396 AC: 60170AN: 151872Hom.: 13049 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
60170
AN:
151872
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
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Gnomad FIN
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Gnomad MID
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Gnomad NFE
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Gnomad OTH
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.396 AC: 60209AN: 151990Hom.: 13060 Cov.: 32 AF XY: 0.395 AC XY: 29356AN XY: 74284 show subpopulations
GnomAD4 genome
AF:
AC:
60209
AN:
151990
Hom.:
Cov.:
32
AF XY:
AC XY:
29356
AN XY:
74284
Gnomad4 AFR
AF:
AC:
0.583406
AN:
0.583406
Gnomad4 AMR
AF:
AC:
0.3246
AN:
0.3246
Gnomad4 ASJ
AF:
AC:
0.345245
AN:
0.345245
Gnomad4 EAS
AF:
AC:
0.38846
AN:
0.38846
Gnomad4 SAS
AF:
AC:
0.266847
AN:
0.266847
Gnomad4 FIN
AF:
AC:
0.37275
AN:
0.37275
Gnomad4 NFE
AF:
AC:
0.315465
AN:
0.315465
Gnomad4 OTH
AF:
AC:
0.364929
AN:
0.364929
Heterozygous variant carriers
0
1783
3565
5348
7130
8913
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
560
1120
1680
2240
2800
<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:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Type 2 diabetes mellitus Uncertain:1
Sep 01, 2014
OMIM
Significance:Uncertain significance
Review Status:no assertion criteria provided
Collection Method:literature only
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism (auto)
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