Variant Effect Prediction

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: rs1801131

Ensembl canonical HGVSC: NM_005957.5:c.1286A>C

Reference genome: GRCh38

Transcript ID: NC_000001.11

Chromosome: 1

Genomic start position: 11794419

Genomic end position: 11794419

Reference allele: T

Alternate allele: G

Disease association with reference allele: False

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	0.009,0.009	B,B	0.14	tolerated	0.201,0.233,0.233,0.201	T,T,T,T	-0.78,-0.78,-0.78,-0.78	T,T,T,T	2.208532	20.9	polymorphism (auto)	simple_aae	0.249401	0.313121	0.151286	0.151297	0.417178	0.219246	0.295	0.1588	0.1555	0.2148	0.3191	0.4153	0.263386	0.167046	0.22052	ALFA Frequency