rs10946398
Variant summary
Our verdict is Benign. Variant got -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 151872 control chromosomes in the gnomAD Genomes database, including 13049 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 ( 13049 hom., cov: 32)
Consequence
CDKAL1
NM_017774.3 intron
NM_017774.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.132
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDKAL1 | NM_017774.3 | c.371+11426A>C | intron_variant | ENST00000274695.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKAL1 | ENST00000274695.8 | c.371+11426A>C | intron_variant | 1 | NM_017774.3 | P1 | |||
CDKAL1 | ENST00000378610.1 | c.371+11426A>C | intron_variant | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.396 AC: 60170AN: 151872Hom.: 13049 Cov.: 32
GnomAD3 genomes
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60170
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32
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Type 2 diabetes mellitus Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | Sep 01, 2014 | - - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at