rs914048941
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_001161352.2(KCNMA1):c.16G>A(p.Gly6Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,523,288 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 Uncertain significance (★★).
Frequency
Consequence
NM_001161352.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000794 AC: 12AN: 151228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000326 AC: 4AN: 122676Hom.: 0 AF XY: 0.0000298 AC XY: 2AN XY: 67130
GnomAD4 exome AF: 0.000135 AC: 185AN: 1372060Hom.: 0 Cov.: 33 AF XY: 0.000124 AC XY: 84AN XY: 676418
GnomAD4 genome AF: 0.0000794 AC: 12AN: 151228Hom.: 0 Cov.: 32 AF XY: 0.0000948 AC XY: 7AN XY: 73814
ClinVar
Submissions by phenotype
not provided Uncertain:3
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In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Inborn genetic diseases Uncertain:1
The c.16G>A (p.G6S) alteration is located in exon 1 (coding exon 1) of the KCNMA1 gene. This alteration results from a G to A substitution at nucleotide position 16, causing the glycine (G) at amino acid position 6 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Generalized epilepsy-paroxysmal dyskinesia syndrome Uncertain:1
This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 6 of the KCNMA1 protein (p.Gly6Ser). 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 KCNMA1-related conditions. ClinVar contains an entry for this variant (Variation ID: 532940). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. -
Intellectual disability Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at