rs6942273

Variant names:

• chr6-21225346-G-A
• rs6942273
• NM_017774.3:c.1549-5502G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-21225346-G-A
• chr6-21225346-G-C

Variant summary

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

The NM_017774.3(CDKAL1):​c.1549-5502G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 151,978 control chromosomes in the GnomAD database, including 33,139 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 0.65 (33139 hom., cov: 31)
• Consequence: CDKAL1 NM_017774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 4 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]

ENSG00000287404 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDKAL1	NM_017774.3	MANE Select	c.1549-5502G>A		intron	N/A	NP_060244.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDKAL1	ENST00000274695.8	TSL:1 MANE Select	c.1549-5502G>A		intron	N/A	ENSP00000274695.4
	CDKAL1	ENST00000378610.1	TSL:2	c.1549-5502G>A		intron	N/A	ENSP00000367873.1
	CDKAL1	ENST00000476517.1	TSL:2	n.247-5502G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98208 AN: 151858 Hom.: 33083 Cov.: 31

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.647 AC: 98319 AN: 151978 Hom.: 33139 Cov.: 31 AF XY: 0.645 AC XY: 47915 AN XY: 74236

African (AFR) AF: 0.854 AC: 35406 AN: 41482

American (AMR) AF: 0.623 AC: 9523 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1553 AN: 3466

East Asian (EAS) AF: 0.573 AC: 2950 AN: 5144

South Asian (SAS) AF: 0.548 AC: 2637 AN: 4810

European-Finnish (FIN) AF: 0.602 AC: 6348 AN: 10542

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.559 AC: 37968 AN: 67948

Other (OTH) AF: 0.618 AC: 1300 AN: 2104

Alfa AF: 0.586 Hom.: 17109

Bravo AF: 0.658

Asia WGS AF: 0.628 AC: 2183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.032
DANN	Benign	0.83
PhyloP100		-0.36
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: rs6942273; hg19: chr6-21225577;