rs2254266

Positions:

• chr10-73841930-T-C

Variant summary

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

The NM_001367534.1(CAMK2G):​c.946+239A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 546,872 control chromosomes in the GnomAD database, including 10,906 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 0.18 (2615 hom., cov: 32)
  • Exomes 𝑓: 0.20 (8291 hom.)
• Consequence: CAMK2G NM_001367534.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443

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]

ENSG00000229990 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK2G	NM_001367534.1	c.946+239A>G		intron_variant		ENST00000423381.6	NP_001354463.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK2G	ENST00000423381.6	c.946+239A>G		intron_variant		5	NM_001367534.1	ENSP00000410298.3

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27613 AN: 152074 Hom.: 2603 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.171

GnomAD4 exome AF: 0.198 AC: 78186 AN: 394680 Hom.: 8291 Cov.: 0 AF XY: 0.203 AC XY: 42376 AN XY: 208378

Gnomad4 AFR exome AF: 0.172

Gnomad4 AMR exome AF: 0.114

Gnomad4 ASJ exome AF: 0.300

Gnomad4 EAS exome AF: 0.214

Gnomad4 SAS exome AF: 0.259

Gnomad4 FIN exome AF: 0.179

Gnomad4 NFE exome AF: 0.189

Gnomad4 OTH exome AF: 0.196

GnomAD4 genome AF: 0.182 AC: 27657 AN: 152192 Hom.: 2615 Cov.: 32 AF XY: 0.179 AC XY: 13328 AN XY: 74408

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.168

Alfa AF: 0.195 Hom.: 5700

Bravo AF: 0.182

Asia WGS AF: 0.198 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.8
DANN	Benign	0.62

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: rs2254266; hg19: chr10-75601688;