rs13234819

Variant names:

• chr7-44303370-G-A
• rs13234819
• NM_001220.5:c.66-19145C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001220.5(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 NM_001220.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.794
• Publications: 5 publications found

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 Gene-Disease associations (from GenCC):

• intellectual disability, autosomal dominant 40

  Inheritance: AD Classification: DEFINITIVE Submitted by: Illumina
• intellectual disability, autosomal dominant 54

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• autosomal dominant non-syndromic intellectual disability

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001220.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMK2B	NM_001220.5	MANE Select	c.66-19145C>T		intron	N/A	NP_001211.3
	CAMK2B	NM_001293170.2		c.66-19145C>T		intron	N/A	NP_001280099.1	Q13554-2
	CAMK2B	NM_172078.3		c.66-19145C>T		intron	N/A	NP_742075.1	Q13554-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMK2B	ENST00000395749.7	TSL:1 MANE Select	c.66-19145C>T		intron	N/A	ENSP00000379098.2	Q13554-1
	CAMK2B	ENST00000440254.6	TSL:1	c.66-19145C>T		intron	N/A	ENSP00000397937.2	Q13554-2
	CAMK2B	ENST00000395747.6	TSL:1	c.66-19145C>T		intron	N/A	ENSP00000379096.2	Q13554-5

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

African (AFR) AF: 0.442 AC: 18310 AN: 41446

American (AMR) AF: 0.333 AC: 5095 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1358 AN: 3472

East Asian (EAS) AF: 0.0576 AC: 298 AN: 5176

South Asian (SAS) AF: 0.283 AC: 1361 AN: 4804

European-Finnish (FIN) AF: 0.382 AC: 4017 AN: 10528

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26878 AN: 67882

Other (OTH) AF: 0.409 AC: 863 AN: 2108

Alfa AF: 0.392 Hom.: 15194

Bravo AF: 0.382

Asia WGS AF: 0.190 AC: 663 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.55
PhyloP100		-0.79
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13234819;

hg19: chr7-44342969;