chr2-165989451-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001165963.4(SCN1A):c.*1794C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000461 in 151,858 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 Uncertain significance (★).
Frequency
Consequence
NM_001165963.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCN1A | ENST00000674923 | c.*1794C>T | 3_prime_UTR_variant | Exon 29 of 29 | NM_001165963.4 | ENSP00000501589.1 | ||||
SCN1A | ENST00000303395 | c.*1794C>T | 3_prime_UTR_variant | Exon 28 of 28 | 5 | ENSP00000303540.4 | ||||
SCN1A | ENST00000375405 | c.*1794C>T | 3_prime_UTR_variant | Exon 26 of 26 | 5 | ENSP00000364554.3 |
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 151858Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 154Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 106
GnomAD4 genome AF: 0.0000461 AC: 7AN: 151858Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74158
ClinVar
Submissions by phenotype
Migraine, familial hemiplegic, 3 Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Generalized epilepsy with febrile seizures plus, type 2 Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at