Variant chr10-73853123-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001367534.1(CAMK2G):c.275+69A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 1,455,384 control chromosomes in the GnomAD database, including 194,584 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.47 ( 17522 hom., cov: 32)

Exomes 𝑓: 0.51 ( 177062 hom. )

Consequence

CAMK2G
NM_001367534.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.151

Variant links:

Genes affected

CAMK2G (HGNC:1463): (calcium/calmodulin dependent protein kinase II gamma) The product of this gene is one of the four subunits of an enzyme which 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 gamma chain. Many alternatively spliced transcripts encoding different isoforms have been described but the full-length nature of all the variants has not been determined.[provided by RefSeq, Mar 2011]

CAMK2G links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

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

BP6

Variant 10-73853123-T-C is Benign according to our data. Variant chr10-73853123-T-C is described in ClinVar as [Benign]. Clinvar id is 1192576.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK2G	NM_001367534.1 linkuse as main transcript	c.275+69A>G		intron_variant		ENST00000423381.6	NP_001354463.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK2G	ENST00000423381.6 linkuse as main transcript	c.275+69A>G		intron_variant		5	NM_001367534.1	ENSP00000410298

Frequencies

GnomAD3 genomes

AF:

0.466

AC:

70826

AN:

151956

Hom.:

17523

Cov.:

show subpopulations

Gnomad AFR

AF:

0.373

Gnomad AMI

AF:

0.529

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.571

Gnomad EAS

AF:

0.115

Gnomad SAS

AF:

0.316

Gnomad FIN

AF:

0.451

Gnomad MID

AF:

0.601

Gnomad NFE

AF:

0.560

Gnomad OTH

AF:

0.533

GnomAD4 exome

AF:

0.509

AC:

663133

AN:

1303310

Hom.:

177062

AF XY:

0.506

AC XY:

332659

AN XY:

656902

show subpopulations

Gnomad4 AFR exome

AF:

0.362

Gnomad4 AMR exome

AF:

0.317

Gnomad4 ASJ exome

AF:

0.564

Gnomad4 EAS exome

AF:

0.119

Gnomad4 SAS exome

AF:

0.330

Gnomad4 FIN exome

AF:

0.447

Gnomad4 NFE exome

AF:

0.555

Gnomad4 OTH exome

AF:

0.497

GnomAD4 genome

AF:

0.466

AC:

70851

AN:

152074

Hom.:

17522

Cov.:

AF XY:

0.459

AC XY:

34111

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.373

Gnomad4 AMR

AF:

0.438

Gnomad4 ASJ

AF:

0.571

Gnomad4 EAS

AF:

0.115

Gnomad4 SAS

AF:

0.317

Gnomad4 FIN

AF:

0.451

Gnomad4 NFE

AF:

0.560

Gnomad4 OTH

AF:

0.529

Alfa

AF:

0.494

Hom.:

2340

Bravo

AF:

0.460

Asia WGS

AF:

0.207

AC:

719

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Intellectual developmental disorder 59

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

DANN

Benign

0.86

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