chr1-196258486-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_198503.5(KCNT2):c.2919A>G(p.Ile973Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000148 in 1,554,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_198503.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNT2 | NM_198503.5 | c.2919A>G | p.Ile973Met | missense_variant | 26/28 | ENST00000294725.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNT2 | ENST00000294725.14 | c.2919A>G | p.Ile973Met | missense_variant | 26/28 | 1 | NM_198503.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000209 AC: 5AN: 238722Hom.: 0 AF XY: 0.0000232 AC XY: 3AN XY: 129362
GnomAD4 exome AF: 0.00000784 AC: 11AN: 1402570Hom.: 0 Cov.: 23 AF XY: 0.0000100 AC XY: 7AN XY: 698926
GnomAD4 genome ? AF: 0.0000789 AC: 12AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74342
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | This alteration is classified as likely 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at