rs7756992

chr6-20679478-A-Gchr6-20679478-A-T

Variant summary

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

The NM_017774(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 151902 control chromosomes in the gnomAD Genomes database, including 11781 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 ( 11781 hom., cov: 32)

Consequence

CDKAL1
NM_017774 intron

Scores

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: -1.87

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=-1.06).

BA1

GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 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+30101A>G		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+30101A>G		intron_variant		1	NM_017774.3	P1	Q5VV42-1
CDKAL1	ENST00000378610.1 linkuse as main transcript	c.371+30101A>G		intron_variant		2		P1	Q5VV42-1

Frequencies

GnomAD3 genomes

AF:

0.371

AC:

56381

AN:

151902

Hom.:

11781

Cov.:

show subpopulations

Gnomad AFR

AF:

0.563

Gnomad AMI

AF:

0.363

Gnomad AMR

AF:

0.311

Gnomad ASJ

AF:

0.316

Gnomad EAS

AF:

0.475

Gnomad SAS

AF:

0.273

Gnomad FIN

AF:

0.350

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.274

Gnomad OTH

AF:

0.346

Alfa

AF:

0.292

Hom.:

15719

Bravo

AF:

0.379

Asia WGS

AF:

0.351

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

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

-1.1

Cadd

Benign

0.65

Dann

Benign

0.47

Splicing

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