rs17151584

Variant names:

• chr10-12361029-A-G
• rs17151584
• NM_153498.4:c.92+11119A>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.92+11119A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0844 in 152,226 control chromosomes in the GnomAD database, including 716 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 0.084 (716 hom., cov: 32)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMK1D	NM_153498.4	c.92+11119A>G		intron_variant	Intron 1 of 10	ENST00000619168.5	NP_705718.1
CAMK1D	NM_020397.4	c.92+11119A>G		intron_variant	Intron 1 of 9		NP_065130.1
CAMK1D	XM_006717482.4	c.92+11119A>G		intron_variant	Intron 1 of 10		XP_006717545.1
CAMK1D	XM_006717483.5	c.92+11119A>G		intron_variant	Intron 1 of 10		XP_006717546.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMK1D	ENST00000619168.5	c.92+11119A>G		intron_variant	Intron 1 of 10	1	NM_153498.4	ENSP00000478874.1
CAMK1D	ENST00000378845.5	c.92+11119A>G		intron_variant	Intron 1 of 9	1		ENSP00000368122.1
CAMK1D	ENST00000487696.1	n.259+11119A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.0845 AC: 12849 AN: 152108 Hom.: 716 Cov.: 32

Gnomad AFR AF: 0.0360

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.0855

Gnomad FIN AF: 0.0803

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0878

Gnomad OTH AF: 0.0760

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

GnomAD4 genome AF: 0.0844 AC: 12849 AN: 152226 Hom.: 716 Cov.: 32 AF XY: 0.0873 AC XY: 6501 AN XY: 74438

African (AFR) AF: 0.0359 AC: 1492 AN: 41564

American (AMR) AF: 0.145 AC: 2213 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 437 AN: 3472

East Asian (EAS) AF: 0.239 AC: 1237 AN: 5168

South Asian (SAS) AF: 0.0854 AC: 412 AN: 4826

European-Finnish (FIN) AF: 0.0803 AC: 852 AN: 10612

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0878 AC: 5974 AN: 68006

Other (OTH) AF: 0.0752 AC: 159 AN: 2114

Alfa AF: 0.0910 Hom.: 1357

Bravo AF: 0.0884

Asia WGS AF: 0.140 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.65
DANN	Benign	0.30
PhyloP100		-0.67
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: rs17151584; hg19: chr10-12403028;