rs1044612

Positions:

• chr10-73813153-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The NM_001367534.1(CAMK2G):​c.*1365G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.014 in 152,834 control chromosomes in the GnomAD database, including 15 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 0.014 (15 hom., cov: 33)
  • Exomes 𝑓: 0.0060 (0 hom.)
• Consequence: CAMK2G NM_001367534.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.809

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.014 (2138/152338) while in subpopulation NFE AF= 0.0247 (1679/68030). AF 95% confidence interval is 0.0237. There are 15 homozygotes in gnomad4. There are 942 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 15 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK2G	NM_001367534.1	c.*1365G>A		3_prime_UTR_variant	23/23	ENST00000423381.6	NP_001354463.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK2G	ENST00000423381	c.*1365G>A		3_prime_UTR_variant	23/23	5	NM_001367534.1	ENSP00000410298.3
CAMK2G	ENST00000322635	c.*1365G>A		3_prime_UTR_variant	21/21	1		ENSP00000315599.3
CAMK2G	ENST00000322680	c.*1365G>A		3_prime_UTR_variant	21/21	5		ENSP00000319060.3
CAMK2G	ENST00000351293	c.*1365G>A		3_prime_UTR_variant	19/19	5		ENSP00000277853.5

Frequencies

GnomAD3 genomes AF: 0.0141 AC: 2141 AN: 152220 Hom.: 15 Cov.: 33

Gnomad AFR AF: 0.00384

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0114

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0105

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0247

Gnomad OTH AF: 0.00766

GnomAD4 exome AF: 0.00605 AC: 3 AN: 496 Hom.: 0 Cov.: 0 AF XY: 0.00680 AC XY: 2 AN XY: 294

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.00225

Gnomad4 NFE exome AF: 0.0278

Gnomad4 OTH exome AF: 0.0714

GnomAD4 genome AF: 0.0140 AC: 2138 AN: 152338 Hom.: 15 Cov.: 33 AF XY: 0.0126 AC XY: 942 AN XY: 74500

Gnomad4 AFR AF: 0.00382

Gnomad4 AMR AF: 0.0114

Gnomad4 ASJ AF: 0.00461

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0106

Gnomad4 FIN AF: 0.00311

Gnomad4 NFE AF: 0.0247

Gnomad4 OTH AF: 0.00758

Alfa AF: 0.0186 Hom.: 6

Bravo AF: 0.0142

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	12
DANN	Benign	0.87

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: rs1044612; hg19: chr10-75572911;