rs2633312

Positions:

• chr10-73871997-T-A

Variant summary

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

The NM_001367534.1(CAMK2G):​c.160+992A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,018 control chromosomes in the GnomAD database, including 17,578 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 0.47 (17578 hom., cov: 31)
• Consequence: CAMK2G NM_001367534.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• 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	c.160+992A>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.160+992A>T		intron_variant		5	NM_001367534.1	ENSP00000410298.3

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70971 AN: 151900 Hom.: 17579 Cov.: 31

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.534

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.467 AC: 70996 AN: 152018 Hom.: 17578 Cov.: 31 AF XY: 0.460 AC XY: 34156 AN XY: 74274

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.529

Alfa AF: 0.502 Hom.: 2469

Bravo AF: 0.461

Asia WGS AF: 0.205 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	14
DANN	Benign	0.69

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: rs2633312; hg19: chr10-75631755;