Variant 3-49860567-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.776-18T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 1,610,700 control chromosomes in the GnomAD database, including 185,740 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.49 ( 19498 hom., cov: 32)

Exomes 𝑓: 0.47 ( 166242 hom. )

Consequence

CAMKV
NM_024046.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0350

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:

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=-0.85).

BP6

Variant 3-49860567-A-G is Benign according to our data. Variant chr3-49860567-A-G is described in ClinVar as [Benign]. Clinvar id is 1269547.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.776-18T>C		intron_variant		ENST00000477224.6	NP_076951.2
CAMKV	NM_001320147.2 linkuse as main transcript	c.776-18T>C		intron_variant			NP_001307076.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMKV	ENST00000477224.6 linkuse as main transcript	c.776-18T>C		intron_variant		1	NM_024046.5	ENSP00000419195	P1	Q8NCB2-1

Frequencies

GnomAD3 genomes

AF:

0.491

AC:

74501

AN:

151836

Hom.:

19474

Cov.:

show subpopulations

Gnomad AFR

AF:

0.634

Gnomad AMI

AF:

0.536

Gnomad AMR

AF:

0.394

Gnomad ASJ

AF:

0.343

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:

0.488

GnomAD3 exomes

AF:

0.399

AC:

97802

AN:

245284

Hom.:

21587

AF XY:

0.396

AC XY:

52506

AN XY:

132558

show subpopulations

Gnomad AFR exome

AF:

0.643

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:

0.387

Gnomad NFE exome

AF:

0.490

Gnomad OTH exome

AF:

0.432

GnomAD4 exome

AF:

0.467

AC:

681716

AN:

1458746

Hom.:

166242

Cov.:

AF XY:

0.461

AC XY:

334512

AN XY:

725406

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:

74573

AN:

151954

Hom.:

19498

Cov.:

AF XY:

0.477

AC XY:

35455

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.634

Gnomad4 AMR

AF:

0.393

Gnomad4 ASJ

AF:

0.343

Gnomad4 EAS

AF:

0.143

Gnomad4 SAS

AF:

0.234

Gnomad4 FIN

AF:

0.382

Gnomad4 NFE

AF:

0.494

Gnomad4 OTH

AF:

0.491

Alfa

AF:

0.474

Hom.:

11005

Bravo

AF:

0.505

Asia WGS

AF:

0.282

AC:

981

AN:

3476

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

9.4

DANN

Benign

0.65

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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