20-45094986-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001322799.2(KCNS1):āc.1465A>Gā(p.Ile489Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 1,613,382 control chromosomes in the GnomAD database, including 160,825 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001322799.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNS1 | NM_001322799.2 | c.1465A>G | p.Ile489Val | missense_variant | 4/4 | ENST00000537075.3 | |
KCNS1 | NM_002251.5 | c.1465A>G | p.Ile489Val | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNS1 | ENST00000537075.3 | c.1465A>G | p.Ile489Val | missense_variant | 4/4 | 1 | NM_001322799.2 | P1 | |
KCNS1 | ENST00000306117.5 | c.1465A>G | p.Ile489Val | missense_variant | 5/5 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.470 AC: 71250AN: 151550Hom.: 17340 Cov.: 29
GnomAD3 exomes AF: 0.409 AC: 102918AN: 251364Hom.: 22515 AF XY: 0.408 AC XY: 55480AN XY: 135850
GnomAD4 exome AF: 0.437 AC: 638464AN: 1461714Hom.: 143446 Cov.: 56 AF XY: 0.433 AC XY: 315022AN XY: 727162
GnomAD4 genome AF: 0.470 AC: 71344AN: 151668Hom.: 17379 Cov.: 29 AF XY: 0.470 AC XY: 34782AN XY: 74072
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at