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_172107.4:c.172C>A
Ensembl canonical HGVSC: NM_172107.4:c.172C>A
Reference genome: GRCh38
Transcript ID: NC_000020.11
Chromosome: 20
Genomic start position: 63472292
Genomic end position: 63472292
Reference allele: G
Alternate allele: T
Disease association with reference allele: False
Variant type: SNV
Gene: KCNQ2
| 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 | None | None | 0.0 | deleterious_low_confidence | 0.151,0.12,0.144,0.142,0.143,0.155,0.15,0.15,0.14 | T,T,T,T,T,T,T,T,T | -5.15,-5.37,-5.23,-5.3,-5.08 | D,D,D,D,D | 2.787282 | 23.0 | polymorphism | simple_aae | None | None | None | None | None | None | None | None | None | None | None | None | None | None | None | No ALFA allele frequency available |