Variant rs10946398 details in Genebe, Genetics Data Aggregator

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

Scores

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: -0.132

Links

CDKAL1 (HGNC:21050):

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 linkuse as main transcript	c.371+11426A>C		intron_variant		ENST00000274695.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDKAL1	ENST00000274695.8 linkuse as main transcript	c.371+11426A>C		intron_variant		1	NM_017774.3	P1	Q5VV42-1
CDKAL1	ENST00000378610.1 linkuse as main transcript	c.371+11426A>C		intron_variant		2		P1	Q5VV42-1

Frequencies

GnomAD3 genomes

AF:

0.396

AC:

60170

AN:

151872

Hom.:

13049

Cov.:

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

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 provided

literature only

OMIM

Sep 01, 2014

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

Cadd

Benign

2.8

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over