chr3-49862362-G-C

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_024046.5(CAMKV):​c.27C>G​(p.Gly9Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G9G) has been classified as Benign.

Frequency

Genomes: not found (cov: 33)

Consequence

CAMKV
NM_024046.5 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.41
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]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP7
Synonymous conserved (PhyloP=-2.41 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CAMKVNM_024046.5 linkc.27C>G p.Gly9Gly synonymous_variant Exon 2 of 11 ENST00000477224.6 NP_076951.2 Q8NCB2-1A0A140VKD5
CAMKVNM_001320147.2 linkc.27C>G p.Gly9Gly synonymous_variant Exon 2 of 12 NP_001307076.1 Q8NCB2-3A0A024R331

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CAMKVENST00000477224.6 linkc.27C>G p.Gly9Gly synonymous_variant Exon 2 of 11 1 NM_024046.5 ENSP00000419195.1 Q8NCB2-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
46
GnomAD4 genome
Cov.:
33
Alfa
AF:
0.00
Hom.:
10542

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
0.27
DANN
Benign
0.63
PhyloP100
-2.4
PromoterAI
-0.025
Neutral

Splicing

Name
Calibrated prediction
Score
Prediction
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

Other links and lift over

dbSNP: rs3796386; hg19: chr3-49899795; API