rs149804567
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP3BP4_StrongBP6_Very_StrongBS1BS2
The NM_020822.3(KCNT1):c.2543A>G(p.Glu848Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00293 in 1,552,002 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_020822.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00231 AC: 352AN: 152172Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00229 AC: 361AN: 157314Hom.: 1 AF XY: 0.00226 AC XY: 187AN XY: 82848
GnomAD4 exome AF: 0.00300 AC: 4200AN: 1399712Hom.: 9 Cov.: 32 AF XY: 0.00287 AC XY: 1981AN XY: 690470
GnomAD4 genome AF: 0.00231 AC: 352AN: 152290Hom.: 1 Cov.: 33 AF XY: 0.00244 AC XY: 182AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:6
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KCNT1: BS1 -
See Variant Classification Assertion Criteria. -
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not specified Benign:4
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Developmental and epileptic encephalopathy, 14 Benign:2
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Developmental and epileptic encephalopathy, 14;C3554306:Autosomal dominant nocturnal frontal lobe epilepsy 5 Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Autosomal dominant nocturnal frontal lobe epilepsy 5 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at