Variant 5-150222800-T-A 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.1467-87A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 1,542,084 control chromosomes in the GnomAD database, including 93,919 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.35 ( 9282 hom., cov: 32)

Exomes 𝑓: 0.35 ( 84637 hom. )

Consequence

CAMK2A
NM_015981.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: -2.99

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:

SLC6A7 (HGNC:11054): (solute carrier family 6 member 7) This gene is a member of the gamma-aminobutyric acid (GABA) neurotransmitter gene family and encodes a high-affinity mammalian brain L-proline transporter protein. This transporter protein differs from other sodium-dependent plasma membrane carriers by its pharmacological specificity, kinetic properties, and ionic requirements. [provided by RefSeq, Jul 2008]

SLC6A7 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=-0.93).

BP6

Variant 5-150222800-T-A is Benign according to our data. Variant chr5-150222800-T-A is described in ClinVar as [Benign]. Clinvar id is 1192688.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK2A	NM_015981.4 linkuse as main transcript	c.1467-87A>T		intron_variant		ENST00000671881.1	NP_057065.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK2A	ENST00000671881.1 linkuse as main transcript	c.1467-87A>T		intron_variant			NM_015981.4	ENSP00000500386	P3	Q9UQM7-2

Frequencies

GnomAD3 genomes

AF:

0.348

AC:

52792

AN:

151882

Hom.:

9280

Cov.:

show subpopulations

Gnomad AFR

AF:

0.361

Gnomad AMI

AF:

0.249

Gnomad AMR

AF:

0.391

Gnomad ASJ

AF:

0.271

Gnomad EAS

AF:

0.168

Gnomad SAS

AF:

0.302

Gnomad FIN

AF:

0.317

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.357

Gnomad OTH

AF:

0.347

GnomAD4 exome

AF:

0.346

AC:

480994

AN:

1390082

Hom.:

84637

Cov.:

AF XY:

0.344

AC XY:

239521

AN XY:

695330

show subpopulations

Gnomad4 AFR exome

AF:

0.354

Gnomad4 AMR exome

AF:

0.462

Gnomad4 ASJ exome

AF:

0.266

Gnomad4 EAS exome

AF:

0.166

Gnomad4 SAS exome

AF:

0.321

Gnomad4 FIN exome

AF:

0.311

Gnomad4 NFE exome

AF:

0.354

Gnomad4 OTH exome

AF:

0.333

GnomAD4 genome

AF:

0.347

AC:

52813

AN:

152002

Hom.:

9282

Cov.:

AF XY:

0.345

AC XY:

25615

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.361

Gnomad4 AMR

AF:

0.391

Gnomad4 ASJ

AF:

0.271

Gnomad4 EAS

AF:

0.168

Gnomad4 SAS

AF:

0.301

Gnomad4 FIN

AF:

0.317

Gnomad4 NFE

AF:

0.357

Gnomad4 OTH

AF:

0.342

Alfa

AF:

0.219

Hom.:

489

Bravo

AF:

0.353

Asia WGS

AF:

0.221

AC:

772

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

-0.93

CADD

Benign

0.089

DANN

Benign

0.61

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