rs7756992
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+30101A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,020 control chromosomes in the GnomAD database, including 11,801 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 0.37 ( 11801 hom., cov: 32)
Consequence
CDKAL1
NM_017774.3 intron
NM_017774.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.87
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=-1.06).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.371 AC: 56381AN: 151902Hom.: 11781 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
56381
AN:
151902
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
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Gnomad ASJ
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Gnomad EAS
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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: 0.371 AC: 56440AN: 152020Hom.: 11801 Cov.: 32 AF XY: 0.374 AC XY: 27767AN XY: 74316 show subpopulations
GnomAD4 genome
AF:
AC:
56440
AN:
152020
Hom.:
Cov.:
32
AF XY:
AC XY:
27767
AN XY:
74316
Gnomad4 AFR
AF:
AC:
0.563254
AN:
0.563254
Gnomad4 AMR
AF:
AC:
0.310462
AN:
0.310462
Gnomad4 ASJ
AF:
AC:
0.316138
AN:
0.316138
Gnomad4 EAS
AF:
AC:
0.474324
AN:
0.474324
Gnomad4 SAS
AF:
AC:
0.273067
AN:
0.273067
Gnomad4 FIN
AF:
AC:
0.350019
AN:
0.350019
Gnomad4 NFE
AF:
AC:
0.274253
AN:
0.274253
Gnomad4 OTH
AF:
AC:
0.3463
AN:
0.3463
Heterozygous variant carriers
0
1683
3366
5048
6731
8414
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
536
1072
1608
2144
2680
<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
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Asia WGS
AF:
AC:
1216
AN:
3472
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