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: rs397507545
Ensembl canonical HGVSC: NM_002834.5:c.1507G>A
Reference genome: GRCh38
Transcript ID: NC_000012.12
Chromosome: 12
Genomic start position: 112489083
Genomic end position: 112489083
Reference allele: G
Alternate allele: A
Disease association with reference allele: False
Variant type: SNV
Gene: PTPN11
| 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 | 0.005,0.004,0.016 | D,D,D | -5.83 | D | 4.38625 | 31.0 | disease causing (ClinVar) | simple_aae | None | None | None | None | None | None | None | None | None | None | None | None | None | None | None | ALFA Frequency |