rs6937610

Variant names:

• chr6-21219206-G-A
• rs6937610
• NM_017774.3:c.1549-11642G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-21219206-G-A
• chr6-21219206-G-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.1549-11642G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,940 control chromosomes in the GnomAD database, including 17,375 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 0.45 (17375 hom., cov: 32)
• Consequence: CDKAL1 NM_017774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 2 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDKAL1	NM_017774.3	c.1549-11642G>A		intron_variant	Intron 15 of 15	ENST00000274695.8	NP_060244.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDKAL1	ENST00000274695.8	c.1549-11642G>A		intron_variant	Intron 15 of 15	1	NM_017774.3	ENSP00000274695.4
CDKAL1	ENST00000378610.1	c.1549-11642G>A		intron_variant	Intron 13 of 13	2		ENSP00000367873.1
CDKAL1	ENST00000476517.1	n.247-11642G>A		intron_variant	Intron 2 of 2	2
ENSG00000287404	ENST00000724722.1	n.280-28518C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67673 AN: 151822 Hom.: 17346 Cov.: 32

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.446 AC: 67754 AN: 151940 Hom.: 17375 Cov.: 32 AF XY: 0.446 AC XY: 33140 AN XY: 74286

African (AFR) AF: 0.708 AC: 29316 AN: 41428

American (AMR) AF: 0.426 AC: 6505 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1012 AN: 3458

East Asian (EAS) AF: 0.564 AC: 2908 AN: 5160

South Asian (SAS) AF: 0.388 AC: 1864 AN: 4808

European-Finnish (FIN) AF: 0.339 AC: 3577 AN: 10552

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21460 AN: 67940

Other (OTH) AF: 0.418 AC: 882 AN: 2112

Alfa AF: 0.388 Hom.: 1613

Bravo AF: 0.463

Asia WGS AF: 0.544 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.57
PhyloP100		-0.12
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: rs6937610; hg19: chr6-21219437;