Variant rs1127065 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001220.5(CAMK2B):c.1791G>C(p.Pro597=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0194 in 1,612,832 control chromosomes in the GnomAD database, including 360 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.014 ( 20 hom., cov: 33)

Exomes 𝑓: 0.020 ( 340 hom. )

Consequence

CAMK2B
NM_001220.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.83

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 -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 7-44220272-C-G is Benign according to our data. Variant chr7-44220272-C-G is described in ClinVar as [Benign]. Clinvar id is 1616494.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-3.83 with no splicing effect.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0141 (2142/152108) while in subpopulation SAS AF= 0.0253 (122/4820). AF 95% confidence interval is 0.0217. There are 20 homozygotes in gnomad4. There are 1054 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High AC in GnomAd4 at 2142 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK2B	NM_001220.5 linkuse as main transcript	c.1791G>C	p.Pro597=	synonymous_variant	23/24	ENST00000395749.7	NP_001211.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK2B	ENST00000395749.7 linkuse as main transcript	c.1791G>C	p.Pro597=	synonymous_variant	23/24	1	NM_001220.5	ENSP00000379098		Q13554-1

Frequencies

GnomAD3 genomes

AF:

0.0141

AC:

2141

AN:

151992

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00413

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00432

Gnomad ASJ

AF:

0.0161

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0251

Gnomad FIN

AF:

0.0330

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0198

Gnomad OTH

AF:

0.0129

GnomAD3 exomes

AF:

0.0170

AC:

4213

AN:

248552

Hom.:

AF XY:

0.0177

AC XY:

2391

AN XY:

134856

show subpopulations

Gnomad AFR exome

AF:

0.00336

Gnomad AMR exome

AF:

0.00490

Gnomad ASJ exome

AF:

0.0126

Gnomad EAS exome

AF:

0.000218

Gnomad SAS exome

AF:

0.0256

Gnomad FIN exome

AF:

0.0390

Gnomad NFE exome

AF:

0.0192

Gnomad OTH exome

AF:

0.0160

GnomAD4 exome

AF:

0.0199

AC:

29112

AN:

1460724

Hom.:

340

Cov.:

AF XY:

0.0202

AC XY:

14702

AN XY:

726648

show subpopulations

Gnomad4 AFR exome

AF:

0.00311

Gnomad4 AMR exome

AF:

0.00561

Gnomad4 ASJ exome

AF:

0.0141

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.0270

Gnomad4 FIN exome

AF:

0.0391

Gnomad4 NFE exome

AF:

0.0205

Gnomad4 OTH exome

AF:

0.0193

GnomAD4 genome

AF:

0.0141

AC:

2142

AN:

152108

Hom.:

Cov.:

AF XY:

0.0142

AC XY:

1054

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.00412

Gnomad4 AMR

AF:

0.00431

Gnomad4 ASJ

AF:

0.0161

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.0253

Gnomad4 FIN

AF:

0.0330

Gnomad4 NFE

AF:

0.0198

Gnomad4 OTH

AF:

0.0128

Alfa

AF:

0.00108

Hom.:

17968

EpiCase

AF:

0.0183

EpiControl

AF:

0.0159

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

7.8

DANN

Benign

0.82

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