Variant chr7-44220107-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001220.5(CAMK2B):c.1956C>T(p.Asn652=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 1,608,392 control chromosomes in the GnomAD database, including 138,307 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.36 ( 10661 hom., cov: 34)

Exomes 𝑓: 0.42 ( 127646 hom. )

Consequence

CAMK2B
NM_001220.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.41

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BP6

Variant 7-44220107-G-A is Benign according to our data. Variant chr7-44220107-G-A is described in ClinVar as [Benign]. Clinvar id is 1192566.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.41 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMK2B	NM_001220.5 linkuse as main transcript	c.1956C>T	p.Asn652=	synonymous_variant	23/24	ENST00000395749.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMK2B	ENST00000395749.7 linkuse as main transcript	c.1956C>T	p.Asn652=	synonymous_variant	23/24	1	NM_001220.5		Q13554-1

Frequencies

GnomAD3 genomes

AF:

0.362

AC:

55027

AN:

152078

Hom.:

10656

Cov.:

show subpopulations

Gnomad AFR

AF:

0.213

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.357

Gnomad ASJ

AF:

0.446

Gnomad EAS

AF:

0.364

Gnomad SAS

AF:

0.440

Gnomad FIN

AF:

0.514

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.422

Gnomad OTH

AF:

0.341

GnomAD3 exomes

AF:

0.406

AC:

97604

AN:

240622

Hom.:

20461

AF XY:

0.411

AC XY:

53892

AN XY:

130988

show subpopulations

Gnomad AFR exome

AF:

0.203

Gnomad AMR exome

AF:

0.374

Gnomad ASJ exome

AF:

0.450

Gnomad EAS exome

AF:

0.347

Gnomad SAS exome

AF:

0.437

Gnomad FIN exome

AF:

0.509

Gnomad NFE exome

AF:

0.423

Gnomad OTH exome

AF:

0.401

GnomAD4 exome

AF:

0.415

AC:

604627

AN:

1456196

Hom.:

127646

Cov.:

AF XY:

0.416

AC XY:

301151

AN XY:

724342

show subpopulations

Gnomad4 AFR exome

AF:

0.200

Gnomad4 AMR exome

AF:

0.369

Gnomad4 ASJ exome

AF:

0.455

Gnomad4 EAS exome

AF:

0.322

Gnomad4 SAS exome

AF:

0.439

Gnomad4 FIN exome

AF:

0.506

Gnomad4 NFE exome

AF:

0.421

Gnomad4 OTH exome

AF:

0.405

GnomAD4 genome

AF:

0.362

AC:

55044

AN:

152196

Hom.:

10661

Cov.:

AF XY:

0.368

AC XY:

27413

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.213

Gnomad4 AMR

AF:

0.357

Gnomad4 ASJ

AF:

0.446

Gnomad4 EAS

AF:

0.364

Gnomad4 SAS

AF:

0.441

Gnomad4 FIN

AF:

0.514

Gnomad4 NFE

AF:

0.422

Gnomad4 OTH

AF:

0.346

Alfa

AF:

0.407

Hom.:

3192

Bravo

AF:

0.339

Asia WGS

AF:

0.387

AC:

1346

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 30, 2020	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

Intellectual disability, autosomal dominant 54

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

4.0

DANN

Benign

0.85

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over