chr1-196280852-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_198503.5(KCNT2):c.2910+8A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00128 in 1,610,636 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_198503.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNT2 | NM_198503.5 | c.2910+8A>G | splice_region_variant, intron_variant | ENST00000294725.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNT2 | ENST00000294725.14 | c.2910+8A>G | splice_region_variant, intron_variant | 1 | NM_198503.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000821 AC: 125AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000789 AC: 198AN: 250890Hom.: 0 AF XY: 0.000818 AC XY: 111AN XY: 135654
GnomAD4 exome AF: 0.00133 AC: 1941AN: 1458292Hom.: 1 Cov.: 28 AF XY: 0.00129 AC XY: 939AN XY: 725708
GnomAD4 genome ? AF: 0.000821 AC: 125AN: 152344Hom.: 0 Cov.: 32 AF XY: 0.000846 AC XY: 63AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | KCNT2: BP4, BS1 - |
KCNT2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at