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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: 11-64750475-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=64750475&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PYGM",
"hgnc_id": 9726,
"hgvs_c": "c.2078T>G",
"hgvs_p": "p.Met693Arg",
"inheritance_mode": "AR,AD",
"pathogenic_score": 9,
"score": 9,
"transcript": "NM_005609.4",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3_Strong",
"acmg_score": 9,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.3105,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.49,
"chr": "11",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9621887803077698,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 842,
"aa_ref": "M",
"aa_start": 693,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2866,
"cdna_start": 2154,
"cds_end": null,
"cds_length": 2529,
"cds_start": 2078,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_005609.4",
"gene_hgnc_id": 9726,
"gene_symbol": "PYGM",
"hgvs_c": "c.2078T>G",
"hgvs_p": "p.Met693Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000164139.4",
"protein_coding": true,
"protein_id": "NP_005600.1",
"strand": false,
"transcript": "NM_005609.4",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 842,
"aa_ref": "M",
"aa_start": 693,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2866,
"cdna_start": 2154,
"cds_end": null,
"cds_length": 2529,
"cds_start": 2078,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000164139.4",
"gene_hgnc_id": 9726,
"gene_symbol": "PYGM",
"hgvs_c": "c.2078T>G",
"hgvs_p": "p.Met693Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005609.4",
"protein_coding": true,
"protein_id": "ENSP00000164139.3",
"strand": false,
"transcript": "ENST00000164139.4",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 875,
"aa_ref": "M",
"aa_start": 726,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2963,
"cdna_start": 2245,
"cds_end": null,
"cds_length": 2628,
"cds_start": 2177,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000967737.1",
"gene_hgnc_id": 9726,
"gene_symbol": "PYGM",
"hgvs_c": "c.2177T>G",
"hgvs_p": "p.Met726Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000637796.1",
"strand": false,
"transcript": "ENST00000967737.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 814,
"aa_ref": "M",
"aa_start": 665,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2782,
"cdna_start": 2070,
"cds_end": null,
"cds_length": 2445,
"cds_start": 1994,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000938870.1",
"gene_hgnc_id": 9726,
"gene_symbol": "PYGM",
"hgvs_c": "c.1994T>G",
"hgvs_p": "p.Met665Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000608929.1",
"strand": false,
"transcript": "ENST00000938870.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 754,
"aa_ref": "M",
"aa_start": 605,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3352,
"cdna_start": 2631,
"cds_end": null,
"cds_length": 2265,
"cds_start": 1814,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NM_001164716.1",
"gene_hgnc_id": 9726,
"gene_symbol": "PYGM",
"hgvs_c": "c.1814T>G",
"hgvs_p": "p.Met605Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001158188.1",
"strand": false,
"transcript": "NM_001164716.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 754,
"aa_ref": "M",
"aa_start": 605,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2611,
"cdna_start": 1890,
"cds_end": null,
"cds_length": 2265,
"cds_start": 1814,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000377432.7",
"gene_hgnc_id": 9726,
"gene_symbol": "PYGM",
"hgvs_c": "c.1814T>G",
"hgvs_p": "p.Met605Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000366650.3",
"strand": false,
"transcript": "ENST00000377432.7",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs200688234",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 9726,
"gene_symbol": "PYGM",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.282,
"pos": 64750475,
"ref": "A",
"revel_prediction": "Pathogenic",
"revel_score": 0.96,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_005609.4"
}
]
}