chr10-12752323-C-T

Position:

• chr10-12752323-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153498.4(CAMK1D):​c.300-8625C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,084 control chromosomes in the GnomAD database, including 4,825 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 0.25 (4825 hom., cov: 32)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMK1D	NM_153498.4	c.300-8625C>T		intron_variant		ENST00000619168.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMK1D	ENST00000619168.5	c.300-8625C>T		intron_variant		1	NM_153498.4	P1
CAMK1D	ENST00000378845.5	c.300-8625C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37436 AN: 151966 Hom.: 4826 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.246 AC: 37450 AN: 152084 Hom.: 4825 Cov.: 32 AF XY: 0.244 AC XY: 18168 AN XY: 74354

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.241

Alfa AF: 0.283 Hom.: 8208

Bravo AF: 0.243

Asia WGS AF: 0.217 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.77

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

Publications

LitVar

Other links and lift over

dbSNP: rs4750255; hg19: chr10-12794322;