chr7-44220086-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001220.5(CAMK2B):c.1977C>T(p.Gly659=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00269 in 1,601,746 control chromosomes in the GnomAD database, including 110 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.013 ( 57 hom., cov: 34)
Exomes 𝑓: 0.0016 ( 53 hom. )
Consequence
CAMK2B
NM_001220.5 synonymous
NM_001220.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.75
Genes affected
CAMK2B (HGNC:1461): (calcium/calmodulin dependent protein kinase II beta) The product of this gene belongs to the serine/threonine protein kinase family and to the Ca(2+)/calmodulin-dependent protein kinase subfamily. Calcium signaling is crucial for several aspects of plasticity at glutamatergic synapses. In mammalian cells, the enzyme is composed of four different chains: alpha, beta, gamma, and delta. The product of this gene is a beta chain. It is possible that distinct isoforms of this chain have different cellular localizations and interact differently with calmodulin. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
?
Variant 7-44220086-G-A is Benign according to our data. Variant chr7-44220086-G-A is described in ClinVar as [Benign]. Clinvar id is 783493.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-4.75 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0134 (2046/152304) while in subpopulation AFR AF= 0.0455 (1892/41560). AF 95% confidence interval is 0.0438. There are 57 homozygotes in gnomad4. There are 943 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2042 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAMK2B | NM_001220.5 | c.1977C>T | p.Gly659= | synonymous_variant | 23/24 | ENST00000395749.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAMK2B | ENST00000395749.7 | c.1977C>T | p.Gly659= | synonymous_variant | 23/24 | 1 | NM_001220.5 |
Frequencies
GnomAD3 genomes ? AF: 0.0134 AC: 2042AN: 152186Hom.: 56 Cov.: 34
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GnomAD3 exomes AF: 0.00372 AC: 856AN: 230216Hom.: 20 AF XY: 0.00274 AC XY: 344AN XY: 125652
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GnomAD4 exome AF: 0.00156 AC: 2255AN: 1449442Hom.: 53 Cov.: 32 AF XY: 0.00141 AC XY: 1019AN XY: 720754
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GnomAD4 genome ? AF: 0.0134 AC: 2046AN: 152304Hom.: 57 Cov.: 34 AF XY: 0.0127 AC XY: 943AN XY: 74458
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
CAMK2B-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 28, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at