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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: 7-116794284-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=116794284&ref=G&alt=A&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": "MET",
"hgnc_id": 7029,
"hgvs_c": "c.3853-1371G>A",
"hgvs_p": null,
"inheritance_mode": "AD,AR,Unknown",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_001127500.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_score": -12,
"allele_count_reference_population": 53276,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.85,
"chr": "7",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8500000238418579,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1390,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6822,
"cdna_start": null,
"cds_end": null,
"cds_length": 4173,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_000245.4",
"gene_hgnc_id": 7029,
"gene_symbol": "MET",
"hgvs_c": "c.3799-1371G>A",
"hgvs_p": null,
"intron_rank": 19,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000397752.8",
"protein_coding": true,
"protein_id": "NP_000236.2",
"strand": true,
"transcript": "NM_000245.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1390,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6822,
"cdna_start": null,
"cds_end": null,
"cds_length": 4173,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000397752.8",
"gene_hgnc_id": 7029,
"gene_symbol": "MET",
"hgvs_c": "c.3799-1371G>A",
"hgvs_p": null,
"intron_rank": 19,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000245.4",
"protein_coding": true,
"protein_id": "ENSP00000380860.3",
"strand": true,
"transcript": "ENST00000397752.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1408,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6876,
"cdna_start": null,
"cds_end": null,
"cds_length": 4227,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000318493.11",
"gene_hgnc_id": 7029,
"gene_symbol": "MET",
"hgvs_c": "c.3853-1371G>A",
"hgvs_p": null,
"intron_rank": 19,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000317272.6",
"strand": true,
"transcript": "ENST00000318493.11",
"transcript_support_level": 1
},
{
"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": 6722,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 20,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000436117.3",
"gene_hgnc_id": 7029,
"gene_symbol": "MET",
"hgvs_c": "n.*1404-1371G>A",
"hgvs_p": null,
"intron_rank": 18,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000410980.2",
"strand": true,
"transcript": "ENST00000436117.3",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1408,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6876,
"cdna_start": null,
"cds_end": null,
"cds_length": 4227,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001127500.3",
"gene_hgnc_id": 7029,
"gene_symbol": "MET",
"hgvs_c": "c.3853-1371G>A",
"hgvs_p": null,
"intron_rank": 19,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001120972.1",
"strand": true,
"transcript": "NM_001127500.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1389,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6962,
"cdna_start": null,
"cds_end": null,
"cds_length": 4170,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000950406.1",
"gene_hgnc_id": 7029,
"gene_symbol": "MET",
"hgvs_c": "c.3796-1371G>A",
"hgvs_p": null,
"intron_rank": 19,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000620465.1",
"strand": true,
"transcript": "ENST00000950406.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1362,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6658,
"cdna_start": null,
"cds_end": null,
"cds_length": 4089,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000917365.1",
"gene_hgnc_id": 7029,
"gene_symbol": "MET",
"hgvs_c": "c.3715-1371G>A",
"hgvs_p": null,
"intron_rank": 19,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000587424.1",
"strand": true,
"transcript": "ENST00000917365.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1298,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6582,
"cdna_start": null,
"cds_end": null,
"cds_length": 3897,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000950407.1",
"gene_hgnc_id": 7029,
"gene_symbol": "MET",
"hgvs_c": "c.3523-1371G>A",
"hgvs_p": null,
"intron_rank": 17,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000620466.1",
"strand": true,
"transcript": "ENST00000950407.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 960,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5608,
"cdna_start": null,
"cds_end": null,
"cds_length": 2883,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 20,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001324402.2",
"gene_hgnc_id": 7029,
"gene_symbol": "MET",
"hgvs_c": "c.2509-1371G>A",
"hgvs_p": null,
"intron_rank": 18,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001311331.1",
"strand": true,
"transcript": "NM_001324402.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1409,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6872,
"cdna_start": null,
"cds_end": null,
"cds_length": 4230,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011516223.2",
"gene_hgnc_id": 7029,
"gene_symbol": "MET",
"hgvs_c": "c.3856-1371G>A",
"hgvs_p": null,
"intron_rank": 20,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011514525.1",
"strand": true,
"transcript": "XM_011516223.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs6951311",
"effect": "intron_variant",
"frequency_reference_population": 0.35034326,
"gene_hgnc_id": 7029,
"gene_symbol": "MET",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": 53276,
"gnomad_genomes_af": 0.350343,
"gnomad_genomes_homalt": 11164,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 11164,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.218,
"pos": 116794284,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001127500.3"
}
]
}