rs10946425

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017774.3(CDKAL1):​c.1055+18052C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,972 control chromosomes in the GnomAD database, including 8,646 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 0.33 ( 8646 hom., cov: 32)

Consequence

CDKAL1
NM_017774.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.417
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CDKAL1NM_017774.3 linkuse as main transcriptc.1055+18052C>T intron_variant ENST00000274695.8 NP_060244.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CDKAL1ENST00000274695.8 linkuse as main transcriptc.1055+18052C>T intron_variant 1 NM_017774.3 ENSP00000274695 P1Q5VV42-1
CDKAL1ENST00000378610.1 linkuse as main transcriptc.1055+18052C>T intron_variant 2 ENSP00000367873 P1Q5VV42-1

Frequencies

GnomAD3 genomes
AF:
0.327
AC:
49651
AN:
151854
Hom.:
8648
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.221
Gnomad AMI
AF:
0.363
Gnomad AMR
AF:
0.382
Gnomad ASJ
AF:
0.393
Gnomad EAS
AF:
0.189
Gnomad SAS
AF:
0.310
Gnomad FIN
AF:
0.334
Gnomad MID
AF:
0.446
Gnomad NFE
AF:
0.384
Gnomad OTH
AF:
0.380
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.327
AC:
49662
AN:
151972
Hom.:
8646
Cov.:
32
AF XY:
0.325
AC XY:
24111
AN XY:
74280
show subpopulations
Gnomad4 AFR
AF:
0.221
Gnomad4 AMR
AF:
0.381
Gnomad4 ASJ
AF:
0.393
Gnomad4 EAS
AF:
0.189
Gnomad4 SAS
AF:
0.309
Gnomad4 FIN
AF:
0.334
Gnomad4 NFE
AF:
0.384
Gnomad4 OTH
AF:
0.376
Alfa
AF:
0.379
Hom.:
19045
Bravo
AF:
0.329
Asia WGS
AF:
0.231
AC:
804
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
9.6
DANN
Benign
0.81

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: rs10946425; hg19: chr6-21018655; API