rs2399866

Variant names:

• chr10-12637492-A-G
• rs2399866
• NM_153498.4:c.225-29244A>G

Variant summary

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

The NM_153498.4(CAMK1D):​c.225-29244A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,752 control chromosomes in the GnomAD database, including 17,246 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 0.47 (17246 hom., cov: 31)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 4 publications found

Genes affected

CAMK1D (HGNC:19341): (calcium/calmodulin dependent protein kinase ID) This gene is a member of the calcium/calmodulin-dependent protein kinase 1 family, a subfamily of the serine/threonine kinases. The encoded protein is a component of the calcium-regulated calmodulin-dependent protein kinase cascade. It has been associated with multiple processes including regulation of granulocyte function, activation of CREB-dependent gene transcription, aldosterone synthesis, differentiation and activation of neutrophil cells, and apoptosis of erythroleukemia cells. Alternatively spliced transcript variants encoding different isoforms of this gene have been described. [provided by RefSeq, Jan 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153498.4. 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
	CAMK1D	NM_153498.4	MANE Select	c.225-29244A>G		intron	N/A	NP_705718.1
	CAMK1D	NM_020397.4		c.225-29244A>G		intron	N/A	NP_065130.1
	CAMK1D	NM_001351032.2		c.-67-29244A>G		intron	N/A	NP_001337961.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMK1D	ENST00000619168.5	TSL:1 MANE Select	c.225-29244A>G		intron	N/A	ENSP00000478874.1
	CAMK1D	ENST00000378845.5	TSL:1	c.225-29244A>G		intron	N/A	ENSP00000368122.1
	CAMK1D	ENST00000487696.1	TSL:3	n.260-29244A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71253 AN: 151634 Hom.: 17235 Cov.: 31

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.470 AC: 71308 AN: 151752 Hom.: 17246 Cov.: 31 AF XY: 0.466 AC XY: 34514 AN XY: 74134

African (AFR) AF: 0.547 AC: 22586 AN: 41324

American (AMR) AF: 0.417 AC: 6351 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1803 AN: 3470

East Asian (EAS) AF: 0.535 AC: 2760 AN: 5156

South Asian (SAS) AF: 0.631 AC: 3033 AN: 4806

European-Finnish (FIN) AF: 0.310 AC: 3259 AN: 10504

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29848 AN: 67942

Other (OTH) AF: 0.499 AC: 1046 AN: 2098

Alfa AF: 0.457 Hom.: 69395

Bravo AF: 0.480

Asia WGS AF: 0.614 AC: 2130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.26
PhyloP100		-0.17
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: rs2399866; hg19: chr10-12679491;