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: rs1801133
Ensembl canonical HGVSC: NM_005957.5:c.665C>T
Reference genome: GRCh38
Transcript ID: NC_000001.11
Chromosome: 1
Genomic start position: 11796321
Genomic end position: 11796321
Reference allele: G
Alternate allele: A
Disease association with reference allele: True
Variant type: SNV
Gene: MTHFR
| 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 | 0.941,0.941 | D,D | 0.0 | deleterious | 0.053,0.048,0.048,0.053 | T,D,D,T | -4.03,-4.03,-4.03,-4.03 | D,D,D,D | 4.039767 | 27.3 | polymorphism (auto) | simple_aae | 0.245407 | 0.364811 | 0.090015 | 0.474063 | 0.118609 | 0.295635 | 0.3037 | 0.1124 | 0.5141 | 0.3052 | 0.345 | 0.1409 | 0.275423 | 0.112086 | 0.30216 | ALFA Frequency |