10-12829168-C-T

Variant names:

• chr10-12829168-C-T
• rs1644394
• NM_153498.4:c.*281C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 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=-0.52).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.369 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMK1D	NM_153498.4	MANE Select	c.*281C>T		3_prime_UTR	Exon 11 of 11	NP_705718.1	Q8IU85-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMK1D	ENST00000619168.5	TSL:1 MANE Select	c.*281C>T		3_prime_UTR	Exon 11 of 11	ENSP00000478874.1	Q8IU85-1

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

African (AFR) AF: 0.324 AC: 1399 AN: 4320

American (AMR) AF: 0.234 AC: 1021 AN: 4356

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 1296 AN: 6054

East Asian (EAS) AF: 0.302 AC: 3236 AN: 10720

South Asian (SAS) AF: 0.415 AC: 4101 AN: 9874

European-Finnish (FIN) AF: 0.255 AC: 2714 AN: 10642

Middle Eastern (MID) AF: 0.289 AC: 232 AN: 802

European-Non Finnish (NFE) AF: 0.248 AC: 25608 AN: 103096

Other (OTH) AF: 0.251 AC: 2721 AN: 10834

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

African (AFR) AF: 0.339 AC: 14045 AN: 41374

American (AMR) AF: 0.259 AC: 3952 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 715 AN: 3472

East Asian (EAS) AF: 0.259 AC: 1338 AN: 5166

South Asian (SAS) AF: 0.384 AC: 1841 AN: 4798

European-Finnish (FIN) AF: 0.249 AC: 2605 AN: 10482

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.250 AC: 16963 AN: 67930

Other (OTH) AF: 0.234 AC: 495 AN: 2114

Alfa AF: 0.261 Hom.: 4467

Bravo AF: 0.277

Asia WGS AF: 0.287 AC: 996 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.7
DANN	Benign	0.70
PhyloP100		2.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1644394; hg19: chr10-12871167;