chr9-135702288-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_020822.3(KCNT1):c.30G>A(p.Pro10Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00786 in 1,608,588 control chromosomes in the GnomAD database, including 87 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_020822.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00524 AC: 797AN: 152038Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.00672 AC: 1581AN: 235382Hom.: 9 AF XY: 0.00764 AC XY: 992AN XY: 129928
GnomAD4 exome AF: 0.00813 AC: 11846AN: 1456432Hom.: 82 Cov.: 32 AF XY: 0.00842 AC XY: 6102AN XY: 724562
GnomAD4 genome AF: 0.00522 AC: 795AN: 152156Hom.: 5 Cov.: 33 AF XY: 0.00531 AC XY: 395AN XY: 74406
ClinVar
Submissions by phenotype
not specified Benign:6
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:2
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KCNT1: BP4, BP7, BS1, BS2 -
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 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. -
Developmental and epileptic encephalopathy, 14 Benign:1
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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