chr7-44223857-T-C

Position:

• chr7-44223857-T-C

Variant summary

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

The NM_001220.5(CAMK2B):​c.1597+2659A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 151,902 control chromosomes in the GnomAD database, including 28,210 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 0.61 (28210 hom., cov: 31)
• Consequence: CAMK2B NM_001220.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

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]

CAMK2B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK2B	NM_001220.5	c.1597+2659A>G		intron_variant		ENST00000395749.7	NP_001211.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK2B	ENST00000395749.7	c.1597+2659A>G		intron_variant		1	NM_001220.5	ENSP00000379098.2

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92471 AN: 151784 Hom.: 28185 Cov.: 31

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.609 AC: 92549 AN: 151902 Hom.: 28210 Cov.: 31 AF XY: 0.613 AC XY: 45542 AN XY: 74236

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.576

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.618

Alfa AF: 0.605 Hom.: 27053

Bravo AF: 0.611

Asia WGS AF: 0.573 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.98
DANN	Benign	0.58

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: rs1003573; hg19: chr7-44263456;