4-113511181-T-C

Variant names:

• chr4-113511181-T-C
• rs13130985
• NM_001321571.2:c.947-1506A>G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001321571.2(CAMK2D):​c.947-1506A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,972 control chromosomes in the GnomAD database, including 32,871 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 0.64 (32871 hom., cov: 32)
• Consequence: CAMK2D NM_001321571.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMK2D	NM_001321571.2	c.947-1506A>G		intron_variant	Intron 12 of 20	ENST00000511664.6	NP_001308500.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMK2D	ENST00000511664.6	c.947-1506A>G		intron_variant	Intron 12 of 20	2	NM_001321571.2	ENSP00000425824.1

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97382 AN: 151856 Hom.: 32816 Cov.: 32

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.641 AC: 97490 AN: 151972 Hom.: 32871 Cov.: 32 AF XY: 0.634 AC XY: 47086 AN XY: 74244

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.630

Alfa AF: 0.604 Hom.: 3384

Bravo AF: 0.669

Asia WGS AF: 0.386 AC: 1341 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	18
DANN	Benign	0.84

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: rs13130985; hg19: chr4-114432337;