chr10-12830881-A-G

Position:

• chr10-12830881-A-G

Variant summary

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

The NM_153498.4(CAMK1D):​c.*1994A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 149,852 control chromosomes in the GnomAD database, including 11,881 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 0.40 (11881 hom., cov: 28)
  • Exomes 𝑓: 0.26 (68 hom.)
  • Failed GnomAD Quality Control
• Consequence: CAMK1D NM_153498.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71

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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK1D	NM_153498.4	c.*1994A>G		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.*1994A>G		3_prime_UTR_variant	11/11	1	NM_153498.4	ENSP00000478874	P1

Frequencies

GnomAD3 genomes AF: 0.396 AC: 59302 AN: 149736 Hom.: 11863 Cov.: 28

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.360

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.259 AC: 326 AN: 1260 Hom.: 68 Cov.: 0 AF XY: 0.261 AC XY: 245 AN XY: 940

Gnomad4 AFR exome AF: 0.286

Gnomad4 AMR exome AF: 0.167

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.176

Gnomad4 SAS exome AF: 0.286

Gnomad4 FIN exome AF: 0.353

Gnomad4 NFE exome AF: 0.265

Gnomad4 OTH exome AF: 0.231

GnomAD4 genome AF: 0.396 AC: 59341 AN: 149852 Hom.: 11881 Cov.: 28 AF XY: 0.397 AC XY: 28953 AN XY: 72972

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.355

Alfa AF: 0.384 Hom.: 1364

Bravo AF: 0.392

Asia WGS AF: 0.353 AC: 1228 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.091
DANN	Benign	0.44

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: rs2431623; hg19: chr10-12872880;