2-165989256-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001165963.4(SCN1A):c.*1989C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 151,996 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001165963.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN1A | ENST00000674923 | c.*1989C>A | 3_prime_UTR_variant | Exon 29 of 29 | NM_001165963.4 | ENSP00000501589.1 | ||||
SCN1A | ENST00000303395 | c.*1989C>A | 3_prime_UTR_variant | Exon 28 of 28 | 5 | ENSP00000303540.4 | ||||
SCN1A | ENST00000375405 | c.*1989C>A | 3_prime_UTR_variant | Exon 26 of 26 | 5 | ENSP00000364554.3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151996Hom.: 0 Cov.: 31
GnomAD4 exome Cov.: 0
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151996Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74212
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at