9-135702288-G-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_020822.3(KCNT1):c.30G>C(p.Pro10=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,608,490 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P10P) has been classified as Benign.
Frequency
Consequence
NM_020822.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNT1 | NM_020822.3 | c.30G>C | p.Pro10= | synonymous_variant | 1/31 | ENST00000371757.7 | |
KCNT1 | NM_001272003.2 | c.30G>C | p.Pro10= | synonymous_variant | 1/31 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNT1 | ENST00000371757.7 | c.30G>C | p.Pro10= | synonymous_variant | 1/31 | 1 | NM_020822.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152038Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000212 AC: 5AN: 235382Hom.: 0 AF XY: 0.0000308 AC XY: 4AN XY: 129928
GnomAD4 exome AF: 0.0000165 AC: 24AN: 1456452Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 724570
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152038Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74278
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 14;C3554306:Autosomal dominant nocturnal frontal lobe epilepsy 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at