Variant 3-49860840-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_024046.5(CAMKV):c.651T>C(p.Asn217Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 1,613,624 control chromosomes in the GnomAD database, including 186,207 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.49 ( 19521 hom., cov: 31)

Exomes 𝑓: 0.47 ( 166686 hom. )

Consequence

CAMKV
NM_024046.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.86

Variant links:

Genes affected

CAMKV (HGNC:28788): (CaM kinase like vesicle associated) Predicted to enable calmodulin binding activity and calmodulin-dependent protein kinase activity. Predicted to be involved in peptidyl-serine phosphorylation. Predicted to be located in cytoplasmic vesicle membrane and plasma membrane. Predicted to be active in glutamatergic synapse and postsynapse. [provided by Alliance of Genome Resources, Apr 2022]

CAMKV links:

CAMKV (HGNC:):

CAMKV links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 3-49860840-A-G is Benign according to our data. Variant chr3-49860840-A-G is described in ClinVar as [Benign]. Clinvar id is 1297960.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMKV	NM_024046.5 linkuse as main transcript	c.651T>C	p.Asn217Asn	synonymous_variant	8/11	ENST00000477224.6	NP_076951.2	Q8NCB2-1A0A140VKD5
CAMKV	NM_001320147.2 linkuse as main transcript	c.651T>C	p.Asn217Asn	synonymous_variant	8/12		NP_001307076.1	Q8NCB2-3A0A024R331

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMKV	ENST00000477224.6 linkuse as main transcript	c.651T>C	p.Asn217Asn	synonymous_variant	8/11	1	NM_024046.5	ENSP00000419195.1		Q8NCB2-1

Frequencies

GnomAD3 genomes

AF:

0.491

AC:

74522

AN:

151856

Hom.:

19497

Cov.:

show subpopulations

Gnomad AFR

AF:

0.634

Gnomad AMI

AF:

0.536

Gnomad AMR

AF:

0.394

Gnomad ASJ

AF:

0.342

Gnomad EAS

AF:

0.144

Gnomad SAS

AF:

0.235

Gnomad FIN

AF:

0.382

Gnomad MID

AF:

0.453

Gnomad NFE

AF:

0.494

Gnomad OTH

AF:

0.489

GnomAD3 exomes

AF:

0.399

AC:

100383

AN:

251356

Hom.:

22421

AF XY:

0.397

AC XY:

53906

AN XY:

135840

show subpopulations

Gnomad AFR exome

AF:

0.644

Gnomad AMR exome

AF:

0.286

Gnomad ASJ exome

AF:

0.343

Gnomad EAS exome

AF:

0.149

Gnomad SAS exome

AF:

0.234

Gnomad FIN exome

AF:

0.386

Gnomad NFE exome

AF:

0.490

Gnomad OTH exome

AF:

0.433

GnomAD4 exome

AF:

0.467

AC:

682994

AN:

1461650

Hom.:

166686

Cov.:

AF XY:

0.461

AC XY:

335292

AN XY:

727124

show subpopulations

Gnomad4 AFR exome

AF:

0.637

Gnomad4 AMR exome

AF:

0.299

Gnomad4 ASJ exome

AF:

0.349

Gnomad4 EAS exome

AF:

0.154

Gnomad4 SAS exome

AF:

0.242

Gnomad4 FIN exome

AF:

0.387

Gnomad4 NFE exome

AF:

0.505

Gnomad4 OTH exome

AF:

0.454

GnomAD4 genome

AF:

0.491

AC:

74594

AN:

151974

Hom.:

19521

Cov.:

AF XY:

0.477

AC XY:

35465

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.634

Gnomad4 AMR

AF:

0.393

Gnomad4 ASJ

AF:

0.342

Gnomad4 EAS

AF:

0.144

Gnomad4 SAS

AF:

0.234

Gnomad4 FIN

AF:

0.382

Gnomad4 NFE

AF:

0.494

Gnomad4 OTH

AF:

0.492

Alfa

AF:

0.485

Hom.:

29662

Bravo

AF:

0.505

Asia WGS

AF:

0.283

AC:

984

AN:

3478

EpiCase

AF:

0.491

EpiControl

AF:

0.491

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 25, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

6.3

DANN

Benign

0.81

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