rs13234819

Positions:

• chr7-44303370-G-A
• chr7-44303370-G-C
• chr7-44303370-G-T

Variant summary

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

The ENST00000395749.7(CAMK2B):​c.66-19145C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,898 control chromosomes in the GnomAD database, including 11,782 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 0.39 (11782 hom., cov: 33)
• Consequence: CAMK2B ENST00000395749.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.794

Genes affected

CAMK2B (HGNC:1461): (calcium/calmodulin dependent protein kinase II beta) 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 beta chain. It is possible that distinct isoforms of this chain have different cellular localizations and interact differently with calmodulin. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK2B	NM_001220.5	c.66-19145C>T		intron_variant		ENST00000395749.7	NP_001211.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK2B	ENST00000395749.7	c.66-19145C>T		intron_variant		1	NM_001220.5	ENSP00000379098

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58550 AN: 151780 Hom.: 11758 Cov.: 33

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.386 AC: 58608 AN: 151898 Hom.: 11782 Cov.: 33 AF XY: 0.381 AC XY: 28297 AN XY: 74232

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.0576

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.409

Alfa AF: 0.393 Hom.: 11674

Bravo AF: 0.382

Asia WGS AF: 0.190 AC: 663 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.55

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: rs13234819; hg19: chr7-44342969;