chr9-135702362-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_020822.3(KCNT1):c.104C>T(p.Ala35Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000652 in 1,609,770 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). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A35D) has been classified as Uncertain significance.
Frequency
Consequence
NM_020822.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNT1 | NM_020822.3 | c.104C>T | p.Ala35Val | missense_variant | 1/31 | ENST00000371757.7 | |
KCNT1 | NM_001272003.2 | c.104C>T | p.Ala35Val | missense_variant | 1/31 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNT1 | ENST00000371757.7 | c.104C>T | p.Ala35Val | missense_variant | 1/31 | 1 | NM_020822.3 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151830Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000572 AC: 14AN: 244620Hom.: 0 AF XY: 0.0000225 AC XY: 3AN XY: 133502
GnomAD4 exome AF: 0.0000700 AC: 102AN: 1457940Hom.: 0 Cov.: 31 AF XY: 0.0000675 AC XY: 49AN XY: 725450
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151830Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74184
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 12, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 18, 2017 | 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. - |
Developmental and epileptic encephalopathy, 14;C3554306:Autosomal dominant nocturnal frontal lobe epilepsy 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | KCNT1: BS1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at