chr10-12833208-C-T

Variant names:

• chr10-12833208-C-T
• rs10906233
• NM_153498.4:c.*4321C>T

Variant summary

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

The NM_153498.4(CAMK1D):​c.*4321C>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 0.0833 in 152,318 control chromosomes in the GnomAD database, including 1,213 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 0.083 (1213 hom., cov: 33)
  • Exomes 𝑓: 0.042 (0 hom.)
• Consequence: CAMK1D NM_153498.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMK1D	NM_153498.4	c.*4321C>T		3_prime_UTR_variant	Exon 11 of 11	ENST00000619168.5	NP_705718.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMK1D	ENST00000619168.5	c.*4321C>T		3_prime_UTR_variant	Exon 11 of 11	1	NM_153498.4	ENSP00000478874.1

Frequencies

GnomAD3 genomes AF: 0.0833 AC: 12667 AN: 152080 Hom.: 1209 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.0383

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0166

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0198

Gnomad OTH AF: 0.0989

GnomAD4 exome AF: 0.0424 AC: 5 AN: 118 Hom.: 0 Cov.: 0 AF XY: 0.0568 AC XY: 5 AN XY: 88

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0288

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0834 AC: 12689 AN: 152200 Hom.: 1213 Cov.: 33 AF XY: 0.0890 AC XY: 6623 AN XY: 74410

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.0383

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0166

Gnomad4 NFE AF: 0.0198

Gnomad4 OTH AF: 0.0970

Alfa AF: 0.0732 Hom.: 174

Bravo AF: 0.100

Asia WGS AF: 0.266 AC: 923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.60

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: rs10906233; hg19: chr10-12875208;