The Variant Effect Prediction table provides variant annotation information, including variant consequences, predicted variant effects and variant allele frequencies. To view live NCBI ALFA allele frequencies for a particular variant, click on the ALFA Frequency link in the table.
Variant Name: NM_001165963.4: c.2522C>T
Ensembl canonical HGVSC: NM_001353948.2:c.2522C>A
Reference genome: GRCh37
Transcript ID: NM_001165963.4
Chromosome: 2
Genomic start position: 166896000
Genomic end position: 166896000
Reference allele: C
Alternate allele: T
Disease association with reference allele: False
Variant type: SNV
Gene: SCN1A
| Consequence terms | Polyphen2 hvar score | Polyphen2 hvar prediction | SIFT score | SIFT prediction | SIFT4G score | SIFT4G prediction | FATHMM score | FATHMM prediction | CADD raw | CADD phred | MutationTaster effect prediction | MutationTaster query model | 1000 Genomes global allele frequency | 1000 Genomes allele frequency EUR | 1000 Genomes allele frequency AFR | 1000 Genomes allele frequency AMR | 1000 Genomes allele frequency SAS | 1000 Genomes allele frequency EAS | ExAC global allele frequency | ExAC allele frequency NFE | ExAC allele frequency AFR | ExAC allele frequency AMR | ExAC allele frequency EAS | ExAC allele frequency SAS | gnomAD global allele frequency | gnomAD allele frequency AFR | gnomAD allele frequency EAS | Live ALFA allele frequency |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| missense_variant | 0.161,0.153,0.161,0.153,0.153 | B,B,B,B,B | 0.02 | deleterious | 0.068,0.068,0.069,0.13 | T,T,T,T | -4.98,-4.98,-4.98,-4.98 | D,D,D,D | None | 23.5 | disease causing | simple_aae | None | None | None | None | None | None | None | None | None | None | None | None | None | None | None | No ALFA allele frequency available |