10-12829168-C-T

Position:

• chr10-12829168-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.*281C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 312,506 control chromosomes in the GnomAD database, including 11,985 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 0.28 (6020 hom., cov: 31)
  • Exomes 𝑓: 0.26 (5965 hom.)
• Consequence: CAMK1D NM_153498.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.61

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=-0.52).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK1D	NM_153498.4	c.*281C>T		3_prime_UTR_variant	11/11	ENST00000619168.5	NP_705718.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK1D	ENST00000619168.5	c.*281C>T		3_prime_UTR_variant	11/11	1	NM_153498.4	ENSP00000478874.1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42200 AN: 151692 Hom.: 6012 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.237

GnomAD4 exome AF: 0.263 AC: 42328 AN: 160698 Hom.: 5965 Cov.: 0 AF XY: 0.268 AC XY: 21956 AN XY: 81874

Gnomad4 AFR exome AF: 0.324

Gnomad4 AMR exome AF: 0.234

Gnomad4 ASJ exome AF: 0.214

Gnomad4 EAS exome AF: 0.302

Gnomad4 SAS exome AF: 0.415

Gnomad4 FIN exome AF: 0.255

Gnomad4 NFE exome AF: 0.248

Gnomad4 OTH exome AF: 0.251

GnomAD4 genome AF: 0.278 AC: 42223 AN: 151808 Hom.: 6020 Cov.: 31 AF XY: 0.280 AC XY: 20766 AN XY: 74180

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.234

Alfa AF: 0.264 Hom.: 3366

Bravo AF: 0.277

Asia WGS AF: 0.287 AC: 996 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.7
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs1644394; hg19: chr10-12871167;