rs17531554

Positions:

• chr4-113583005-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.275+26147G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,250 control chromosomes in the GnomAD database, including 1,403 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 0.12 (1403 hom., cov: 33)
• Consequence: CAMK2D NM_001321571.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

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=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK2D	NM_001321571.2	c.275+26147G>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.275+26147G>A		intron_variant		2	NM_001321571.2	ENSP00000425824

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18913 AN: 152132 Hom.: 1404 Cov.: 33

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0996

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.124 AC: 18906 AN: 152250 Hom.: 1403 Cov.: 33 AF XY: 0.122 AC XY: 9114 AN XY: 74436

Gnomad4 AFR AF: 0.0505

Gnomad4 AMR AF: 0.0994

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.0216

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.130

Alfa AF: 0.142 Hom.: 282

Bravo AF: 0.114

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	11
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: rs17531554; hg19: chr4-114504161;