rs9465922

Positions:

• chr6-20865366-C-A
• chr6-20865366-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017774.3(CDKAL1):​c.742+19188C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.92 in 152,168 control chromosomes in the GnomAD database, including 64,638 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 0.92 (64638 hom., cov: 31)
• Consequence: CDKAL1 NM_017774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDKAL1	NM_017774.3	c.742+19188C>A		intron_variant		ENST00000274695.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDKAL1	ENST00000274695.8	c.742+19188C>A		intron_variant		1	NM_017774.3	P1
CDKAL1	ENST00000378610.1	c.742+19188C>A		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.920 AC: 139895 AN: 152050 Hom.: 64594 Cov.: 31

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.914

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.920 AC: 139995 AN: 152168 Hom.: 64638 Cov.: 31 AF XY: 0.922 AC XY: 68604 AN XY: 74406

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.932

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.919

Gnomad4 FIN AF: 0.990

Gnomad4 NFE AF: 0.953

Gnomad4 OTH AF: 0.915

Alfa AF: 0.941 Hom.: 20675

Bravo AF: 0.912

Asia WGS AF: 0.940 AC: 3271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.6
DANN	Benign	0.78

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

Other links and lift over

dbSNP: rs9465922; hg19: chr6-20865597;