Genetic Variant CAMK2G:c.*498T>A (chr10-73814020-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001367534.1(CAMK2G):c.*498T>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 0.129 in 152,496 control chromosomes in the GnomAD database, including 1,356 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 0.13 ( 1356 hom., cov: 32)

Exomes 𝑓: 0.15 ( 0 hom. )

Consequence

CAMK2G
NM_001367534.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.30

Publications

11 publications found

Variant links:

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 links:

CAMK2G-AS1 (HGNC:56057): (CAMK2G antisense RNA 1)

CAMK2G-AS1 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMK2G	NM_001367534.1 link	c.*498T>A		3_prime_UTR_variant	Exon 23 of 23	ENST00000423381.6	NP_001354463.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMK2G	ENST00000423381.6 link	c.*498T>A		3_prime_UTR_variant	Exon 23 of 23	5	NM_001367534.1	ENSP00000410298.3		H0Y6G2

Frequencies

GnomAD3 genomes

AF:

0.129

AC:

19569

AN:

152070

Hom.:

1341

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.174

Gnomad AMR

AF:

0.102

Gnomad ASJ

AF:

0.210

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.193

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.132

Gnomad OTH

AF:

0.125

GnomAD4 exome

AF:

0.149

AC:

AN:

308

Hom.:

Cov.:

AF XY:

0.153

AC XY:

AN XY:

196

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.151

AC:

AN:

298

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.523

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.129

AC:

19617

AN:

152188

Hom.:

1356

Cov.:

AF XY:

0.129

AC XY:

9563

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.117

AC:

4865

AN:

41524

American (AMR)

AF:

0.102

AC:

1557

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.210

AC:

728

AN:

3470

East Asian (EAS)

AF:

0.125

AC:

647

AN:

5166

South Asian (SAS)

AF:

0.193

AC:

933

AN:

4824

European-Finnish (FIN)

AF:

0.133

AC:

1410

AN:

10594

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.132

AC:

9007

AN:

68000

Other (OTH)

AF:

0.123

AC:

259

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

865

1731

2596

3462

4327

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

222

444

666

888

1110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.135

Hom.:

196

Bravo

AF:

0.127

Asia WGS

AF:

0.149

AC:

520

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

(source)

DANN

Benign

0.67

PhyloP100

1.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over