rs987694

chr4-113697446-G-A

Variant summary

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

The NM_001321571.2(CAMK2D):c.161-35674C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,926 control chromosomes in the GnomAD database, including 10,756 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 0.35 (10756 hom., cov: 32)
• Consequence: CAMK2D NM_001321571.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMK2D	NM_001321571.2	c.161-35674C>T		intron_variant		ENST00000511664.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMK2D	ENST00000511664.6	c.161-35674C>T		intron_variant		2	NM_001321571.2

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53795 AN: 151808 Hom.: 10748 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.354 AC: 53818 AN: 151926 Hom.: 10756 Cov.: 32 AF XY: 0.361 AC XY: 26791 AN XY: 74268

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.344

Alfa AF: 0.393 Hom.: 15948

Bravo AF: 0.347

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	-0.86
Cadd	Benign	3.2
Dann	Benign	0.76

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: rs987694; hg19: chr4-114618602;