4-113458223-C-T

Position:

• chr4-113458223-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.1307-660G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 151,990 control chromosomes in the GnomAD database, including 33,043 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 0.65 (33043 hom., cov: 32)
• Consequence: CAMK2D NM_001321571.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK2D	NM_001321571.2	c.1307-660G>A		intron_variant		ENST00000511664.6	NP_001308500.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK2D	ENST00000511664.6	c.1307-660G>A		intron_variant		2	NM_001321571.2	ENSP00000425824

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98230 AN: 151872 Hom.: 32983 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.634

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.647 AC: 98352 AN: 151990 Hom.: 33043 Cov.: 32 AF XY: 0.645 AC XY: 47913 AN XY: 74270

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.636

Alfa AF: 0.587 Hom.: 25657

Bravo AF: 0.667

Asia WGS AF: 0.652 AC: 2268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.38

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: rs1880529; hg19: chr4-114379379;