rs2664282

chr10-73860999-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001367534.1(CAMK2G):c.161-110A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 771,000 control chromosomes in the GnomAD database, including 93,655 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.43 (15902 hom., cov: 33)
  • Exomes 𝑓: 0.48 (77753 hom.)
• Consequence: CAMK2G NM_001367534.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.18

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 10-73860999-T-C is Benign according to our data. Variant chr10-73860999-T-C is described in ClinVar as [Benign]. Clinvar id is 1192577.Status of the report is criteria_provided_single_submitter, 1 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	UniProt
CAMK2G	NM_001367534.1	c.161-110A>G		intron_variant		ENST00000423381.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMK2G	ENST00000423381.6	c.161-110A>G		intron_variant		5	NM_001367534.1

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65966 AN: 152008 Hom.: 15904 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.518

GnomAD4 exome AF: 0.480 AC: 297214 AN: 618874 Hom.: 77753 AF XY: 0.478 AC XY: 157605 AN XY: 329974

Gnomad4 AFR exome AF: 0.259

Gnomad4 AMR exome AF: 0.332

Gnomad4 ASJ exome AF: 0.564

Gnomad4 EAS exome AF: 0.120

Gnomad4 SAS exome AF: 0.332

Gnomad4 FIN exome AF: 0.448

Gnomad4 NFE exome AF: 0.561

Gnomad4 OTH exome AF: 0.491

GnomAD4 genome AF: 0.434 AC: 65978 AN: 152126 Hom.: 15902 Cov.: 33 AF XY: 0.428 AC XY: 31835 AN XY: 74364

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.514

Alfa AF: 0.543 Hom.: 22176

Bravo AF: 0.424

Asia WGS AF: 0.205 AC: 712 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Intellectual developmental disorder 59 Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	15
Dann	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs2664282; hg19: chr10-75620757; COSMIC: COSV59486541; COSMIC: COSV59486541;