rs10946403

chr6-20717173-A-G

Variant summary

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

The NM_017774.3(CDKAL1):c.372-22346A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,630 control chromosomes in the GnomAD database, including 8,699 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 0.30 (8699 hom., cov: 30)
• Consequence: CDKAL1 NM_017774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDKAL1	NM_017774.3	c.372-22346A>G		intron_variant		ENST00000274695.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDKAL1	ENST00000274695.8	c.372-22346A>G		intron_variant		1	NM_017774.3	P1
CDKAL1	ENST00000378610.1	c.372-22346A>G		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45571 AN: 151512 Hom.: 8675 Cov.: 30

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.301 AC: 45636 AN: 151630 Hom.: 8699 Cov.: 30 AF XY: 0.300 AC XY: 22251 AN XY: 74092

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.287

Alfa AF: 0.214 Hom.: 4882

Bravo AF: 0.319

Asia WGS AF: 0.322 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.7
Dann	Benign	0.51

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: rs10946403; hg19: chr6-20717404;