6-21231243-C-G

Variant names:

• chr6-21231243-C-G
• rs1563727
• NM_017774.3:c.*204C>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.*204C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 418,386 control chromosomes in the GnomAD database, including 84,638 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 0.61 (28249 hom., cov: 31)
  • Exomes 𝑓: 0.65 (56389 hom.)
• Consequence: CDKAL1 NM_017774.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

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]

ENSG00000287404 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDKAL1	NM_017774.3	c.*204C>G		3_prime_UTR_variant	Exon 16 of 16	ENST00000274695.8	NP_060244.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDKAL1	ENST00000274695.8	c.*204C>G		3_prime_UTR_variant	Exon 16 of 16	1	NM_017774.3	ENSP00000274695.4

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91929 AN: 151792 Hom.: 28233 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.599

GnomAD4 exome AF: 0.647 AC: 172360 AN: 266476 Hom.: 56389 Cov.: 3 AF XY: 0.648 AC XY: 87941 AN XY: 135782

African (AFR) AF: 0.496 AC: 4226 AN: 8528

American (AMR) AF: 0.613 AC: 5934 AN: 9680

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 6107 AN: 9688

East Asian (EAS) AF: 0.803 AC: 19641 AN: 24458

South Asian (SAS) AF: 0.666 AC: 4596 AN: 6906

European-Finnish (FIN) AF: 0.711 AC: 14665 AN: 20630

Middle Eastern (MID) AF: 0.624 AC: 819 AN: 1312

European-Non Finnish (NFE) AF: 0.628 AC: 105616 AN: 168202

Other (OTH) AF: 0.630 AC: 10756 AN: 17072

GnomAD4 genome AF: 0.606 AC: 91988 AN: 151910 Hom.: 28249 Cov.: 31 AF XY: 0.613 AC XY: 45475 AN XY: 74222

African (AFR) AF: 0.496 AC: 20556 AN: 41406

American (AMR) AF: 0.625 AC: 9543 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2160 AN: 3470

East Asian (EAS) AF: 0.797 AC: 4119 AN: 5170

South Asian (SAS) AF: 0.700 AC: 3361 AN: 4804

European-Finnish (FIN) AF: 0.711 AC: 7488 AN: 10528

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42803 AN: 67950

Other (OTH) AF: 0.600 AC: 1266 AN: 2110

Alfa AF: 0.497 Hom.: 1452

Bravo AF: 0.591

Asia WGS AF: 0.737 AC: 2561 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	2.0
DANN	Benign	0.79
PhyloP100		0.010
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

Publications

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Other links and lift over

dbSNP: rs1563727; hg19: chr6-21231474;