rs2688626

Variant names:

• chr10-73851332-G-A
• rs2688626
• NM_001367534.1:c.341+922C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-73851332-G-A
• chr10-73851332-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367534.1(CAMK2G):​c.341+922C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,934 control chromosomes in the GnomAD database, including 32,666 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 0.64 (32666 hom., cov: 30)
• Consequence: CAMK2G NM_001367534.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 14 publications found

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 Gene-Disease associations (from GenCC):

• intellectual developmental disorder 59

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P, Illumina
• genetic developmental and epileptic encephalopathy

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMK2G	NM_001367534.1	c.341+922C>T		intron_variant	Intron 5 of 22	ENST00000423381.6	NP_001354463.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMK2G	ENST00000423381.6	c.341+922C>T		intron_variant	Intron 5 of 22	5	NM_001367534.1	ENSP00000410298.3

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97320 AN: 151816 Hom.: 32661 Cov.: 30

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.641 AC: 97348 AN: 151934 Hom.: 32666 Cov.: 30 AF XY: 0.632 AC XY: 46927 AN XY: 74252

African (AFR) AF: 0.491 AC: 20350 AN: 41432

American (AMR) AF: 0.568 AC: 8663 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 3115 AN: 3462

East Asian (EAS) AF: 0.372 AC: 1911 AN: 5142

South Asian (SAS) AF: 0.580 AC: 2796 AN: 4818

European-Finnish (FIN) AF: 0.615 AC: 6489 AN: 10546

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51649 AN: 67954

Other (OTH) AF: 0.701 AC: 1484 AN: 2116

Alfa AF: 0.685 Hom.: 5153

Bravo AF: 0.631

Asia WGS AF: 0.422 AC: 1472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.18
DANN	Benign	0.77
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2688626; hg19: chr10-75611090;