rs9929

chr4-113453977-C-T

Variant summary

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

The NM_001321571.2(CAMK2D):c.*568G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0417 in 152,298 control chromosomes in the GnomAD database, including 182 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 0.042 (182 hom., cov: 31)
  • Exomes 𝑓: 0.029 (0 hom.)
• Consequence: CAMK2D NM_001321571.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

Genes affected

CAMK2D (HGNC:1462): (calcium/calmodulin dependent protein kinase II delta) The product of this gene belongs to the serine/threonine protein kinase family and to the Ca(2+)/calmodulin-dependent protein kinase subfamily. Calcium signaling is crucial for several aspects of plasticity at glutamatergic synapses. In mammalian cells, the enzyme is composed of four different chains: alpha, beta, gamma, and delta. The product of this gene is a delta chain. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Distinct isoforms of this chain have different expression patterns.[provided by RefSeq, Nov 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMK2D	NM_001321571.2	c.*568G>A		3_prime_UTR_variant	21/21	ENST00000511664.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMK2D	ENST00000511664.6	c.*568G>A		3_prime_UTR_variant	21/21	2	NM_001321571.2

Frequencies

GnomAD3 genomes AF: 0.0417 AC: 6334 AN: 151738 Hom.: 183 Cov.: 31

Gnomad AFR AF: 0.0115

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0466

Gnomad ASJ AF: 0.0553

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0742

Gnomad FIN AF: 0.0332

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.0500

GnomAD4 exome AF: 0.0293 AC: 13 AN: 444 Hom.: 0 Cov.: 0 AF XY: 0.0301 AC XY: 8 AN XY: 266

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.0302

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0417 AC: 6331 AN: 151854 Hom.: 182 Cov.: 31 AF XY: 0.0407 AC XY: 3022 AN XY: 74218

Gnomad4 AFR AF: 0.0115

Gnomad4 AMR AF: 0.0466

Gnomad4 ASJ AF: 0.0553

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0738

Gnomad4 FIN AF: 0.0332

Gnomad4 NFE AF: 0.0597

Gnomad4 OTH AF: 0.0495

Alfa AF: 0.0488 Hom.: 30

Bravo AF: 0.0399

Asia WGS AF: 0.0260 AC: 90 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	6.8
Dann	Benign	0.73

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: rs9929; hg19: chr4-114375133;