rs377687237
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_020822.3(KCNT1):c.50C>T(p.Ala17Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000168 in 1,609,672 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). Synonymous variant affecting the same amino acid position (i.e. A17A) has been classified as Likely benign.
Frequency
Consequence
NM_020822.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNT1 | NM_020822.3 | c.50C>T | p.Ala17Val | missense_variant | 1/31 | ENST00000371757.7 | |
KCNT1 | NM_001272003.2 | c.50C>T | p.Ala17Val | missense_variant | 1/31 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNT1 | ENST00000371757.7 | c.50C>T | p.Ala17Val | missense_variant | 1/31 | 1 | NM_020822.3 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151750Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000837 AC: 2AN: 239052Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131340
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1457922Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 725306
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151750Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74098
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2024 | - - |
Developmental and epileptic encephalopathy, 14;C3554306:Autosomal dominant nocturnal frontal lobe epilepsy 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at