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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: 4-74132767-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=74132767&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "MTHFD2L",
"hgnc_id": 31865,
"hgvs_c": "c.-66+7250C>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_001351310.2",
"verdict": "Benign"
},
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000304759",
"hgnc_id": 58816,
"hgvs_c": "n.208+5360G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -12,
"transcript": "ENST00000806138.1",
"verdict": "Benign"
},
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LOC105377277",
"hgnc_id": null,
"hgvs_c": "n.69+5360G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -12,
"transcript": "XR_938878.2",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_score": -12,
"allele_count_reference_population": 73108,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.94,
"chr": "4",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.9399999976158142,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 786,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000429335.5",
"gene_hgnc_id": 31865,
"gene_symbol": "MTHFD2L",
"hgvs_c": "n.-107+7250C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000409391.1",
"strand": true,
"transcript": "ENST00000429335.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1407,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000433372.5",
"gene_hgnc_id": 31865,
"gene_symbol": "MTHFD2L",
"hgvs_c": "n.80+7250C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000433372.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 228,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1699,
"cdna_start": null,
"cds_end": null,
"cds_length": 687,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001351310.2",
"gene_hgnc_id": 31865,
"gene_symbol": "MTHFD2L",
"hgvs_c": "c.-66+7250C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001338239.1",
"strand": true,
"transcript": "NM_001351310.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 228,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1665,
"cdna_start": null,
"cds_end": null,
"cds_length": 687,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001351311.2",
"gene_hgnc_id": 31865,
"gene_symbol": "MTHFD2L",
"hgvs_c": "c.-32+7250C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001338240.1",
"strand": true,
"transcript": "NM_001351311.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 456,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6830,
"cdna_start": null,
"cds_end": null,
"cds_length": 1371,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017008218.3",
"gene_hgnc_id": 31865,
"gene_symbol": "MTHFD2L",
"hgvs_c": "c.-3831+7250C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016863707.1",
"strand": true,
"transcript": "XM_017008218.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 295,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2550,
"cdna_start": null,
"cds_end": null,
"cds_length": 888,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 12,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047415712.1",
"gene_hgnc_id": 31865,
"gene_symbol": "MTHFD2L",
"hgvs_c": "c.-141+7250C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271668.1",
"strand": true,
"transcript": "XM_047415712.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 295,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2475,
"cdna_start": null,
"cds_end": null,
"cds_length": 888,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047415713.1",
"gene_hgnc_id": 31865,
"gene_symbol": "MTHFD2L",
"hgvs_c": "c.-66+7250C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271669.1",
"strand": true,
"transcript": "XM_047415713.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 295,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2441,
"cdna_start": null,
"cds_end": null,
"cds_length": 888,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047415714.1",
"gene_hgnc_id": 31865,
"gene_symbol": "MTHFD2L",
"hgvs_c": "c.-32+7250C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271670.1",
"strand": true,
"transcript": "XM_047415714.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 289,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2476,
"cdna_start": null,
"cds_end": null,
"cds_length": 870,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047415715.1",
"gene_hgnc_id": 31865,
"gene_symbol": "MTHFD2L",
"hgvs_c": "c.-141+7250C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271671.1",
"strand": true,
"transcript": "XM_047415715.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 247,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2350,
"cdna_start": null,
"cds_end": null,
"cds_length": 744,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047415716.1",
"gene_hgnc_id": 31865,
"gene_symbol": "MTHFD2L",
"hgvs_c": "c.-141+7250C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271672.1",
"strand": true,
"transcript": "XM_047415716.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 228,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1721,
"cdna_start": null,
"cds_end": null,
"cds_length": 687,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047415717.1",
"gene_hgnc_id": 31865,
"gene_symbol": "MTHFD2L",
"hgvs_c": "c.-141+7250C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271673.1",
"strand": true,
"transcript": "XM_047415717.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1798,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000429519.5",
"gene_hgnc_id": 31865,
"gene_symbol": "MTHFD2L",
"hgvs_c": "n.458+7250C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000429519.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 954,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000475291.5",
"gene_hgnc_id": 31865,
"gene_symbol": "MTHFD2L",
"hgvs_c": "n.163+7250C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000475291.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
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"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 689,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000490698.5",
"gene_hgnc_id": 31865,
"gene_symbol": "MTHFD2L",
"hgvs_c": "n.229+7250C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000490698.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 474,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000806138.1",
"gene_hgnc_id": 58816,
"gene_symbol": "ENSG00000304759",
"hgvs_c": "n.208+5360G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000806138.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 516,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_938878.2",
"gene_hgnc_id": null,
"gene_symbol": "LOC105377277",
"hgvs_c": "n.69+5360G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_938878.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs7686861",
"effect": "intron_variant",
"frequency_reference_population": 0.48091674,
"gene_hgnc_id": 31865,
"gene_symbol": "MTHFD2L",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": 73108,
"gnomad_genomes_af": 0.480917,
"gnomad_genomes_homalt": 20712,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 20712,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.21,
"pos": 74132767,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_001351310.2"
}
]
}