Variant 5-150223261-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_015981.4(CAMK2A):c.1238-44G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 1,476,122 control chromosomes in the GnomAD database, including 222,905 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.47 ( 18552 hom., cov: 31)

Exomes 𝑓: 0.55 ( 204353 hom. )

Consequence

CAMK2A
NM_015981.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: -0.527

Variant links:

Genes affected

CAMK2A (HGNC:1460): (calcium/calmodulin dependent protein kinase II alpha) The product of this gene belongs to the serine/threonine protein kinases family, and to the Ca(2+)/calmodulin-dependent protein kinases subfamily. Calcium signaling is crucial for several aspects of plasticity at glutamatergic synapses. This calcium calmodulin-dependent protein kinase is composed of four different chains: alpha, beta, gamma, and delta. The alpha chain encoded by this gene is required for hippocampal long-term potentiation (LTP) and spatial learning. In addition to its calcium-calmodulin (CaM)-dependent activity, this protein can undergo autophosphorylation, resulting in CaM-independent activity. Several transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jun 2018]

CAMK2A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 5-150223261-C-T is Benign according to our data. Variant chr5-150223261-C-T is described in ClinVar as [Benign]. Clinvar id is 1192690.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMK2A	NM_015981.4 linkuse as main transcript	c.1238-44G>A		intron_variant		ENST00000671881.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMK2A	ENST00000671881.1 linkuse as main transcript	c.1238-44G>A		intron_variant			NM_015981.4	P3	Q9UQM7-2

Frequencies

GnomAD3 genomes

AF:

0.469

AC:

71264

AN:

151810

Hom.:

18547

Cov.:

show subpopulations

Gnomad AFR

AF:

0.223

Gnomad AMI

AF:

0.610

Gnomad AMR

AF:

0.517

Gnomad ASJ

AF:

0.608

Gnomad EAS

AF:

0.626

Gnomad SAS

AF:

0.495

Gnomad FIN

AF:

0.614

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.562

Gnomad OTH

AF:

0.501

GnomAD3 exomes

AF:

0.537

AC:

117021

AN:

217732

Hom.:

31869

AF XY:

0.543

AC XY:

64292

AN XY:

118396

show subpopulations

Gnomad AFR exome

AF:

0.225

Gnomad AMR exome

AF:

0.483

Gnomad ASJ exome

AF:

0.624

Gnomad EAS exome

AF:

0.617

Gnomad SAS exome

AF:

0.500

Gnomad FIN exome

AF:

0.628

Gnomad NFE exome

AF:

0.572

Gnomad OTH exome

AF:

0.563

GnomAD4 exome

AF:

0.551

AC:

729794

AN:

1324194

Hom.:

204353

Cov.:

AF XY:

0.551

AC XY:

365227

AN XY:

662766

show subpopulations

Gnomad4 AFR exome

AF:

0.213

Gnomad4 AMR exome

AF:

0.482

Gnomad4 ASJ exome

AF:

0.616

Gnomad4 EAS exome

AF:

0.646

Gnomad4 SAS exome

AF:

0.492

Gnomad4 FIN exome

AF:

0.617

Gnomad4 NFE exome

AF:

0.562

Gnomad4 OTH exome

AF:

0.546

GnomAD4 genome

AF:

0.469

AC:

71282

AN:

151928

Hom.:

18552

Cov.:

AF XY:

0.474

AC XY:

35232

AN XY:

74254

show subpopulations

Gnomad4 AFR

AF:

0.223

Gnomad4 AMR

AF:

0.517

Gnomad4 ASJ

AF:

0.608

Gnomad4 EAS

AF:

0.626

Gnomad4 SAS

AF:

0.496

Gnomad4 FIN

AF:

0.614

Gnomad4 NFE

AF:

0.562

Gnomad4 OTH

AF:

0.502

Alfa

AF:

0.553

Hom.:

32309

Bravo

AF:

0.452

Asia WGS

AF:

0.537

AC:

1867

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Intellectual disability, autosomal recessive 63

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Intellectual disability, autosomal dominant 53

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

5.8

DANN

Benign

0.72

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over