rs7766070

Variant names:

• chr6-20686342-C-A
• rs7766070
• NM_017774.3:c.371+36965C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 53 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017774.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDKAL1	NM_017774.3	MANE Select	c.371+36965C>A		intron	N/A	NP_060244.2	Q5VV42-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDKAL1	ENST00000274695.8	TSL:1 MANE Select	c.371+36965C>A		intron	N/A	ENSP00000274695.4	Q5VV42-1
	CDKAL1	ENST00000946780.1		c.371+36965C>A		intron	N/A	ENSP00000616839.1
	CDKAL1	ENST00000378610.1	TSL:2	c.371+36965C>A		intron	N/A	ENSP00000367873.1	Q5VV42-1

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

African (AFR) AF: 0.193 AC: 7978 AN: 41406

American (AMR) AF: 0.241 AC: 3668 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 974 AN: 3470

East Asian (EAS) AF: 0.377 AC: 1929 AN: 5110

South Asian (SAS) AF: 0.269 AC: 1293 AN: 4806

European-Finnish (FIN) AF: 0.349 AC: 3674 AN: 10538

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18408 AN: 67934

Other (OTH) AF: 0.249 AC: 524 AN: 2108

Alfa AF: 0.158 Hom.: 699

Bravo AF: 0.244

Asia WGS AF: 0.299 AC: 1035 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.5
DANN	Benign	0.89
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7766070; hg19: chr6-20686573;