rs7738382

Variant names:

• chr6-20746005-C-A
• rs7738382
• NM_017774.3:c.468+6390C>A

Variant summary

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

The NM_017774.3(CDKAL1):​c.468+6390C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,016 control chromosomes in the GnomAD database, including 32,087 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 0.64 (32087 hom., cov: 32)
• Consequence: CDKAL1 NM_017774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 10 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.722 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.468+6390C>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.468+6390C>A		intron	N/A	ENSP00000274695.4	Q5VV42-1
	CDKAL1	ENST00000946780.1		c.468+6390C>A		intron	N/A	ENSP00000616839.1
	CDKAL1	ENST00000378610.1	TSL:2	c.468+6390C>A		intron	N/A	ENSP00000367873.1	Q5VV42-1

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97476 AN: 151896 Hom.: 32080 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.938

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.642 AC: 97527 AN: 152016 Hom.: 32087 Cov.: 32 AF XY: 0.640 AC XY: 47530 AN XY: 74310

African (AFR) AF: 0.482 AC: 19986 AN: 41442

American (AMR) AF: 0.658 AC: 10045 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2486 AN: 3472

East Asian (EAS) AF: 0.533 AC: 2755 AN: 5172

South Asian (SAS) AF: 0.599 AC: 2882 AN: 4810

European-Finnish (FIN) AF: 0.711 AC: 7513 AN: 10574

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.727 AC: 49441 AN: 67968

Other (OTH) AF: 0.648 AC: 1370 AN: 2114

Alfa AF: 0.695 Hom.: 62858

Bravo AF: 0.632

Asia WGS AF: 0.553 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.048
DANN	Benign	0.23
PhyloP100		-1.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs7738382; hg19: chr6-20746236;