NM_017774.3:c.1056-27665A>G

Variant names:

• chr6-21037383-A-G
• rs9295488
• NM_017774.3:c.1056-27665A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017774.3(CDKAL1):​c.1056-27665A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,078 control chromosomes in the GnomAD database, including 6,125 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 0.28 (6125 hom., cov: 32)
• Consequence: CDKAL1 NM_017774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDKAL1	NM_017774.3	c.1056-27665A>G		intron_variant	Intron 11 of 15	ENST00000274695.8	NP_060244.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDKAL1	ENST00000274695.8	c.1056-27665A>G		intron_variant	Intron 11 of 15	1	NM_017774.3	ENSP00000274695.4
CDKAL1	ENST00000378610.1	c.1056-27665A>G		intron_variant	Intron 9 of 13	2		ENSP00000367873.1

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42107 AN: 151960 Hom.: 6116 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.277 AC: 42134 AN: 152078 Hom.: 6125 Cov.: 32 AF XY: 0.280 AC XY: 20821 AN XY: 74352

African (AFR) AF: 0.236 AC: 9789 AN: 41484

American (AMR) AF: 0.314 AC: 4794 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 866 AN: 3468

East Asian (EAS) AF: 0.131 AC: 680 AN: 5180

South Asian (SAS) AF: 0.361 AC: 1740 AN: 4826

European-Finnish (FIN) AF: 0.321 AC: 3392 AN: 10578

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19890 AN: 67960

Other (OTH) AF: 0.295 AC: 620 AN: 2104

Alfa AF: 0.289 Hom.: 856

Bravo AF: 0.271

Asia WGS AF: 0.274 AC: 950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.85
DANN	Benign	0.77
PhyloP100		-0.011
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: rs9295488; hg19: chr6-21037614;