3-49862362-G-A

Variant names:

• chr3-49862362-G-A
• rs3796386
• NM_024046.5:c.27C>T

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_024046.5(CAMKV):​c.27C>T​(p.Gly9Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 1,613,286 control chromosomes in the GnomAD database, including 124,094 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.36 (10490 hom., cov: 33)
  • Exomes 𝑓: 0.39 (113604 hom.)
• Consequence: CAMKV NM_024046.5 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.41

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 -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP6: Variant 3-49862362-G-A is Benign according to our data. Variant chr3-49862362-G-A is described in ClinVar as [Benign]. Clinvar id is 1270206.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-2.41 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMKV	NM_024046.5	c.27C>T	p.Gly9Gly	synonymous_variant	Exon 2 of 11	ENST00000477224.6	NP_076951.2
CAMKV	NM_001320147.2	c.27C>T	p.Gly9Gly	synonymous_variant	Exon 2 of 12		NP_001307076.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMKV	ENST00000477224.6	c.27C>T	p.Gly9Gly	synonymous_variant	Exon 2 of 11	1	NM_024046.5	ENSP00000419195.1

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55180 AN: 151946 Hom.: 10485 Cov.: 33

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.366

GnomAD2 exomes AF: 0.321 AC: 80770 AN: 251422 AF XY: 0.322

Gnomad AFR exome AF: 0.365

Gnomad AMR exome AF: 0.241

Gnomad ASJ exome AF: 0.267

Gnomad EAS exome AF: 0.122

Gnomad FIN exome AF: 0.319

Gnomad NFE exome AF: 0.416

Gnomad OTH exome AF: 0.356

GnomAD4 exome AF: 0.385 AC: 562747 AN: 1461222 Hom.: 113604 Cov.: 46 AF XY: 0.380 AC XY: 276438 AN XY: 726952

African (AFR) AF: 0.356 AC: 11905 AN: 33468

American (AMR) AF: 0.251 AC: 11216 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 7032 AN: 26130

East Asian (EAS) AF: 0.133 AC: 5285 AN: 39700

South Asian (SAS) AF: 0.173 AC: 14935 AN: 86248

European-Finnish (FIN) AF: 0.321 AC: 17101 AN: 53354

Middle Eastern (MID) AF: 0.351 AC: 2025 AN: 5768

European-Non Finnish (NFE) AF: 0.424 AC: 471027 AN: 1111452

Other (OTH) AF: 0.368 AC: 22221 AN: 60380

GnomAD4 genome AF: 0.363 AC: 55205 AN: 152064 Hom.: 10490 Cov.: 33 AF XY: 0.354 AC XY: 26320 AN XY: 74380

African (AFR) AF: 0.360 AC: 14934 AN: 41432

American (AMR) AF: 0.328 AC: 5017 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 913 AN: 3468

East Asian (EAS) AF: 0.118 AC: 612 AN: 5166

South Asian (SAS) AF: 0.166 AC: 803 AN: 4830

European-Finnish (FIN) AF: 0.316 AC: 3341 AN: 10580

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28308 AN: 67988

Other (OTH) AF: 0.369 AC: 779 AN: 2110

Alfa AF: 0.390 Hom.: 10542

Bravo AF: 0.369

Asia WGS AF: 0.205 AC: 712 AN: 3478

EpiCase AF: 0.414

EpiControl AF: 0.418

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Apr 08, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.31
DANN	Benign	0.80
PhyloP100		-2.4
PromoterAI		-0.010	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
Splicevardb		2.0
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Other links and lift over

dbSNP: rs3796386; hg19: chr3-49899795; COSMIC: COSV56554568; COSMIC: COSV56554568;