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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 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

Scores

2

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: -0.132
Variant links:
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 made for transcript

Verdict is Benign. Variant got -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

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CDKAL1NM_017774.3 linkuse as main transcriptc.371+11426A>C intron_variant ENST00000274695.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CDKAL1ENST00000274695.8 linkuse as main transcriptc.371+11426A>C intron_variant 1 NM_017774.3 P1Q5VV42-1
CDKAL1ENST00000378610.1 linkuse as main transcriptc.371+11426A>C intron_variant 2 P1Q5VV42-1

Frequencies

GnomAD3 genomes
AF:
0.396
AC:
60170
AN:
151872
Hom.:
13049
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.584
Gnomad AMI
AF:
0.377
Gnomad AMR
AF:
0.325
Gnomad ASJ
AF:
0.345
Gnomad EAS
AF:
0.389
Gnomad SAS
AF:
0.266
Gnomad FIN
AF:
0.373
Gnomad MID
AF:
0.341
Gnomad NFE
AF:
0.316
Gnomad OTH
AF:
0.365
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.396
AC:
60209
AN:
151990
Hom.:
13060
Cov.:
32
AF XY:
0.395
AC XY:
29356
AN XY:
74284
show subpopulations
Gnomad4 AFR
AF:
0.583
Gnomad4 AMR
AF:
0.325
Gnomad4 ASJ
AF:
0.345
Gnomad4 EAS
AF:
0.388
Gnomad4 SAS
AF:
0.267
Gnomad4 FIN
AF:
0.373
Gnomad4 NFE
AF:
0.315
Gnomad4 OTH
AF:
0.365
Alfa
AF:
0.325
Hom.:
11318
Bravo
AF:
0.400

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 providedliterature onlyOMIMSep 01, 2014- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
Cadd
Benign
4.0
Dann
Benign
0.42

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10946398; hg19: chr6-20661034; API