7-44220124-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP2
The NM_001220.5(CAMK2B):c.1939G>A(p.Asp647Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000621 in 1,611,454 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. D647D) has been classified as Likely benign.
Frequency
Consequence
NM_001220.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAMK2B | NM_001220.5 | c.1939G>A | p.Asp647Asn | missense_variant | 23/24 | ENST00000395749.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAMK2B | ENST00000395749.7 | c.1939G>A | p.Asp647Asn | missense_variant | 23/24 | 1 | NM_001220.5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152244Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000816 AC: 2AN: 245026Hom.: 0 AF XY: 0.00000750 AC XY: 1AN XY: 133346
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1459210Hom.: 0 Cov.: 55 AF XY: 0.00000413 AC XY: 3AN XY: 725930
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152244Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74378
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 10, 2018 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 647 of the CAMK2B protein (p.Asp647Asn). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with CAMK2B-related conditions. ClinVar contains an entry for this variant (Variation ID: 985763). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at