rs9821675

Positions:

• chr3-49865111-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024046.5(CAMKV):​c.-14-2709T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 152,132 control chromosomes in the GnomAD database, including 19,740 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 0.49 (19740 hom., cov: 33)
• Consequence: CAMKV NM_024046.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMKV	NM_024046.5	c.-14-2709T>C		intron_variant		ENST00000477224.6	NP_076951.2
CAMKV	NM_001320147.2	c.-14-2709T>C		intron_variant			NP_001307076.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMKV	ENST00000477224.6	c.-14-2709T>C		intron_variant		1	NM_024046.5	ENSP00000419195.1

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74895 AN: 152014 Hom.: 19710 Cov.: 33

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.490

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.493 AC: 74974 AN: 152132 Hom.: 19740 Cov.: 33 AF XY: 0.479 AC XY: 35643 AN XY: 74366

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.493

Alfa AF: 0.497 Hom.: 3933

Bravo AF: 0.507

Asia WGS AF: 0.288 AC: 999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	2.6
DANN	Benign	0.55

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

Other links and lift over

dbSNP: rs9821675; hg19: chr3-49902544;