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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 5-79119261-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=79119261&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 79119261,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_001713.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BHMT",
"gene_hgnc_id": 1047,
"hgvs_c": "c.169C>T",
"hgvs_p": "p.Arg57Cys",
"transcript": "NM_001713.3",
"protein_id": "NP_001704.2",
"transcript_support_level": null,
"aa_start": 57,
"aa_end": null,
"aa_length": 406,
"cds_start": 169,
"cds_end": null,
"cds_length": 1221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000274353.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001713.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BHMT",
"gene_hgnc_id": 1047,
"hgvs_c": "c.169C>T",
"hgvs_p": "p.Arg57Cys",
"transcript": "ENST00000274353.10",
"protein_id": "ENSP00000274353.5",
"transcript_support_level": 1,
"aa_start": 57,
"aa_end": null,
"aa_length": 406,
"cds_start": 169,
"cds_end": null,
"cds_length": 1221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001713.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000274353.10"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BHMT",
"gene_hgnc_id": 1047,
"hgvs_c": "c.169C>T",
"hgvs_p": "p.Arg57Cys",
"transcript": "ENST00000910530.1",
"protein_id": "ENSP00000580589.1",
"transcript_support_level": null,
"aa_start": 57,
"aa_end": null,
"aa_length": 405,
"cds_start": 169,
"cds_end": null,
"cds_length": 1218,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910530.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BHMT",
"gene_hgnc_id": 1047,
"hgvs_c": "c.169C>T",
"hgvs_p": "p.Arg57Cys",
"transcript": "ENST00000910525.1",
"protein_id": "ENSP00000580584.1",
"transcript_support_level": null,
"aa_start": 57,
"aa_end": null,
"aa_length": 404,
"cds_start": 169,
"cds_end": null,
"cds_length": 1215,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910525.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BHMT",
"gene_hgnc_id": 1047,
"hgvs_c": "c.169C>T",
"hgvs_p": "p.Arg57Cys",
"transcript": "ENST00000910528.1",
"protein_id": "ENSP00000580587.1",
"transcript_support_level": null,
"aa_start": 57,
"aa_end": null,
"aa_length": 404,
"cds_start": 169,
"cds_end": null,
"cds_length": 1215,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910528.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BHMT",
"gene_hgnc_id": 1047,
"hgvs_c": "c.169C>T",
"hgvs_p": "p.Arg57Cys",
"transcript": "ENST00000910529.1",
"protein_id": "ENSP00000580588.1",
"transcript_support_level": null,
"aa_start": 57,
"aa_end": null,
"aa_length": 368,
"cds_start": 169,
"cds_end": null,
"cds_length": 1107,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910529.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BHMT",
"gene_hgnc_id": 1047,
"hgvs_c": "c.169C>T",
"hgvs_p": "p.Arg57Cys",
"transcript": "ENST00000910526.1",
"protein_id": "ENSP00000580585.1",
"transcript_support_level": null,
"aa_start": 57,
"aa_end": null,
"aa_length": 354,
"cds_start": 169,
"cds_end": null,
"cds_length": 1065,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910526.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BHMT",
"gene_hgnc_id": 1047,
"hgvs_c": "c.169C>T",
"hgvs_p": "p.Arg57Cys",
"transcript": "ENST00000910527.1",
"protein_id": "ENSP00000580586.1",
"transcript_support_level": null,
"aa_start": 57,
"aa_end": null,
"aa_length": 345,
"cds_start": 169,
"cds_end": null,
"cds_length": 1038,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910527.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "BHMT",
"gene_hgnc_id": 1047,
"hgvs_c": "c.166+3362C>T",
"hgvs_p": null,
"transcript": "ENST00000524080.1",
"protein_id": "ENSP00000428240.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 253,
"cds_start": null,
"cds_end": null,
"cds_length": 762,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000524080.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BHMT",
"gene_hgnc_id": 1047,
"hgvs_c": "n.246C>T",
"hgvs_p": null,
"transcript": "ENST00000520703.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000520703.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124901012",
"gene_hgnc_id": null,
"hgvs_c": "n.55G>A",
"hgvs_p": null,
"transcript": "XR_007058837.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007058837.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "DMGDH",
"gene_hgnc_id": 24475,
"hgvs_c": "n.491+1080G>A",
"hgvs_p": null,
"transcript": "ENST00000520388.5",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000520388.5"
}
],
"gene_symbol": "BHMT",
"gene_hgnc_id": 1047,
"dbsnp": "rs372610894",
"frequency_reference_population": 0.000028717082,
"hom_count_reference_population": 0,
"allele_count_reference_population": 46,
"gnomad_exomes_af": 0.000028973,
"gnomad_genomes_af": 0.0000262798,
"gnomad_exomes_ac": 42,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8704881072044373,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.409,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1286,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.18,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.788,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001713.3",
"gene_symbol": "BHMT",
"hgnc_id": 1047,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.169C>T",
"hgvs_p": "p.Arg57Cys"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007058837.1",
"gene_symbol": "LOC124901012",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.55G>A",
"hgvs_p": null
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000520388.5",
"gene_symbol": "DMGDH",
"hgnc_id": 24475,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.491+1080G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}