3-49865111-A-G

Variant names:

• chr3-49865111-A-G
• rs9821675
• NM_024046.5:c.-14-2709T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024046.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMKV	NM_024046.5	MANE Select	c.-14-2709T>C		intron	N/A	NP_076951.2
	CAMKV	NM_001320147.2		c.-14-2709T>C		intron	N/A	NP_001307076.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMKV	ENST00000477224.6	TSL:1 MANE Select	c.-14-2709T>C		intron	N/A	ENSP00000419195.1
	CAMKV	ENST00000296471.11	TSL:1	c.-14-2709T>C		intron	N/A	ENSP00000296471.6
	CAMKV	ENST00000475665.5	TSL:1	n.147-2709T>C		intron	N/A

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

African (AFR) AF: 0.647 AC: 26822 AN: 41462

American (AMR) AF: 0.393 AC: 6004 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1174 AN: 3466

East Asian (EAS) AF: 0.144 AC: 746 AN: 5180

South Asian (SAS) AF: 0.236 AC: 1140 AN: 4830

European-Finnish (FIN) AF: 0.383 AC: 4052 AN: 10588

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33376 AN: 67992

Other (OTH) AF: 0.493 AC: 1043 AN: 2114

Alfa AF: 0.480 Hom.: 6864

Bravo AF: 0.507

Asia WGS AF: 0.288 AC: 999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	2.6
DANN	Benign	0.55
PhyloP100		0.074
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9821675; hg19: chr3-49902544;