rs7766070

Positions:

• chr6-20686342-C-A
• chr6-20686342-C-G
• chr6-20686342-C-T

Variant summary

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

The NM_017774.3(CDKAL1):​c.371+36965C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,824 control chromosomes in the GnomAD database, including 5,189 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 0.26 (5189 hom., cov: 31)
• Consequence: CDKAL1 NM_017774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDKAL1	NM_017774.3	c.371+36965C>A		intron_variant		ENST00000274695.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDKAL1	ENST00000274695.8	c.371+36965C>A		intron_variant		1	NM_017774.3	P1
CDKAL1	ENST00000378610.1	c.371+36965C>A		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38862 AN: 151706 Hom.: 5184 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.256 AC: 38865 AN: 151824 Hom.: 5189 Cov.: 31 AF XY: 0.263 AC XY: 19472 AN XY: 74170

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.249

Alfa AF: 0.267 Hom.: 681

Bravo AF: 0.244

Asia WGS AF: 0.299 AC: 1035 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.5
DANN	Benign	0.89

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: rs7766070; hg19: chr6-20686573;