rs755284666
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6
The ENST00000286628.14(KCNMA1):āc.1218A>Gā(p.Gly406=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000143 in 1,613,136 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: š 0.000053 ( 0 hom., cov: 32)
Exomes š: 0.000010 ( 0 hom. )
Consequence
KCNMA1
ENST00000286628.14 synonymous
ENST00000286628.14 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.66
Genes affected
KCNMA1 (HGNC:6284): (potassium calcium-activated channel subfamily M alpha 1) This gene encodes the alpha subunit of calcium-activated BK channel. The encoded protein is involved in several physiological processes including smooth muscle contraction, neurotransmitter release and neuronal excitability. Mutations in this gene are associated with a spectrum of neurological disorders including Paroxysmal Nonkinesigenic Dyskinesia 3, Idiopathic Generalized Epilepsy 16 and Liang-Wang syndrome. [provided by RefSeq, Aug 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BP6
Variant 10-77108486-T-C is Benign according to our data. Variant chr10-77108486-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 502293.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=2, Likely_benign=1}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNMA1 | NM_001161352.2 | c.1218A>G | p.Gly406= | synonymous_variant | 9/28 | ENST00000286628.14 | NP_001154824.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNMA1 | ENST00000286628.14 | c.1218A>G | p.Gly406= | synonymous_variant | 9/28 | 1 | NM_001161352.2 | ENSP00000286628 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 151970Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251402Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135874
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GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461166Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726950
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GnomAD4 genome AF: 0.0000526 AC: 8AN: 151970Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74210
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:2Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 26, 2017 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Apr 19, 2023 | Has not been previously published as pathogenic or benign to our knowledge; In silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown. - |
Generalized epilepsy-paroxysmal dyskinesia syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 04, 2023 | - - |
Computational scores
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Benign
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Details are displayed if max score is > 0.2
DS_DL_spliceai
Position offset: -5
Find out detailed SpliceAI scores and Pangolin per-transcript scores at