rs2242255

Positions:

• chr10-73837531-T-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001367534.1(CAMK2G):​c.1010-20A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 1,603,904 control chromosomes in the GnomAD database, including 29,082 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 (2485 hom., cov: 32)
  • Exomes 𝑓: 0.19 (26597 hom.)
• Consequence: CAMK2G NM_001367534.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK2G	NM_001367534.1	c.1010-20A>T		intron_variant		ENST00000423381.6	NP_001354463.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK2G	ENST00000423381.6	c.1010-20A>T		intron_variant		5	NM_001367534.1	ENSP00000410298.3

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26868 AN: 151940 Hom.: 2473 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.164

GnomAD3 exomes AF: 0.189 AC: 47533 AN: 251492 Hom.: 4809 AF XY: 0.195 AC XY: 26467 AN XY: 135922

Gnomad AFR exome AF: 0.173

Gnomad AMR exome AF: 0.115

Gnomad ASJ exome AF: 0.308

Gnomad EAS exome AF: 0.218

Gnomad SAS exome AF: 0.253

Gnomad FIN exome AF: 0.162

Gnomad NFE exome AF: 0.186

Gnomad OTH exome AF: 0.197

GnomAD4 exome AF: 0.188 AC: 272816 AN: 1451846 Hom.: 26597 Cov.: 28 AF XY: 0.191 AC XY: 137929 AN XY: 722946

Gnomad4 AFR exome AF: 0.169

Gnomad4 AMR exome AF: 0.115

Gnomad4 ASJ exome AF: 0.304

Gnomad4 EAS exome AF: 0.217

Gnomad4 SAS exome AF: 0.252

Gnomad4 FIN exome AF: 0.169

Gnomad4 NFE exome AF: 0.183

Gnomad4 OTH exome AF: 0.195

GnomAD4 genome AF: 0.177 AC: 26913 AN: 152058 Hom.: 2485 Cov.: 32 AF XY: 0.175 AC XY: 13001 AN XY: 74344

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.161

Alfa AF: 0.196 Hom.: 559

Bravo AF: 0.177

Asia WGS AF: 0.195 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	18
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

Other links and lift over

dbSNP: rs2242255; hg19: chr10-75597289; COSMIC: COSV59480692; COSMIC: COSV59480692;