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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: 9-100296933-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=100296933&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 13,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "INVS",
"hgnc_id": 17870,
"hgvs_c": "c.2803C>T",
"hgvs_p": "p.His935Tyr",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -13,
"transcript": "NM_014425.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_score": -13,
"allele_count_reference_population": 4522,
"alphamissense_prediction": null,
"alphamissense_score": 0.096,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.52,
"chr": "9",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Infantile nephronophthisis,Nephronophthisis,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.007744967937469482,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1065,
"aa_ref": "H",
"aa_start": 935,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4897,
"cdna_start": 3001,
"cds_end": null,
"cds_length": 3198,
"cds_start": 2803,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NM_014425.5",
"gene_hgnc_id": 17870,
"gene_symbol": "INVS",
"hgvs_c": "c.2803C>T",
"hgvs_p": "p.His935Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000262457.7",
"protein_coding": true,
"protein_id": "NP_055240.2",
"strand": true,
"transcript": "NM_014425.5",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1065,
"aa_ref": "H",
"aa_start": 935,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4897,
"cdna_start": 3001,
"cds_end": null,
"cds_length": 3198,
"cds_start": 2803,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000262457.7",
"gene_hgnc_id": 17870,
"gene_symbol": "INVS",
"hgvs_c": "c.2803C>T",
"hgvs_p": "p.His935Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_014425.5",
"protein_coding": true,
"protein_id": "ENSP00000262457.2",
"strand": true,
"transcript": "ENST00000262457.7",
"transcript_support_level": 1
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1065,
"aa_ref": "H",
"aa_start": 935,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8845,
"cdna_start": 3052,
"cds_end": null,
"cds_length": 3198,
"cds_start": 2803,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000885857.1",
"gene_hgnc_id": 17870,
"gene_symbol": "INVS",
"hgvs_c": "c.2803C>T",
"hgvs_p": "p.His935Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000555916.1",
"strand": true,
"transcript": "ENST00000885857.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1065,
"aa_ref": "H",
"aa_start": 935,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3631,
"cdna_start": 3096,
"cds_end": null,
"cds_length": 3198,
"cds_start": 2803,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000885859.1",
"gene_hgnc_id": 17870,
"gene_symbol": "INVS",
"hgvs_c": "c.2803C>T",
"hgvs_p": "p.His935Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000555918.1",
"strand": true,
"transcript": "ENST00000885859.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1065,
"aa_ref": "H",
"aa_start": 935,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4901,
"cdna_start": 3496,
"cds_end": null,
"cds_length": 3198,
"cds_start": 2803,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000951904.1",
"gene_hgnc_id": 17870,
"gene_symbol": "INVS",
"hgvs_c": "c.2803C>T",
"hgvs_p": "p.His935Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621963.1",
"strand": true,
"transcript": "ENST00000951904.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1063,
"aa_ref": "H",
"aa_start": 933,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3475,
"cdna_start": 2939,
"cds_end": null,
"cds_length": 3192,
"cds_start": 2797,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000951905.1",
"gene_hgnc_id": 17870,
"gene_symbol": "INVS",
"hgvs_c": "c.2797C>T",
"hgvs_p": "p.His933Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621964.1",
"strand": true,
"transcript": "ENST00000951905.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 1009,
"aa_ref": "H",
"aa_start": 879,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4713,
"cdna_start": 2817,
"cds_end": null,
"cds_length": 3030,
"cds_start": 2635,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000885858.1",
"gene_hgnc_id": 17870,
"gene_symbol": "INVS",
"hgvs_c": "c.2635C>T",
"hgvs_p": "p.His879Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000555917.1",
"strand": true,
"transcript": "ENST00000885858.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 969,
"aa_ref": "H",
"aa_start": 839,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4985,
"cdna_start": 3089,
"cds_end": null,
"cds_length": 2910,
"cds_start": 2515,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "NM_001318381.2",
"gene_hgnc_id": 17870,
"gene_symbol": "INVS",
"hgvs_c": "c.2515C>T",
"hgvs_p": "p.His839Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001305310.1",
"strand": true,
"transcript": "NM_001318381.2",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 895,
"aa_ref": "H",
"aa_start": 765,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2968,
"cdna_start": 2459,
"cds_end": null,
"cds_length": 2688,
"cds_start": 2293,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000262456.6",
"gene_hgnc_id": 17870,
"gene_symbol": "INVS",
"hgvs_c": "c.2293C>T",
"hgvs_p": "p.His765Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000262456.2",
"strand": true,
"transcript": "ENST00000262456.6",
"transcript_support_level": 5
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 739,
"aa_ref": "H",
"aa_start": 609,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4908,
"cdna_start": 3012,
"cds_end": null,
"cds_length": 2220,
"cds_start": 1825,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NM_001318382.2",
"gene_hgnc_id": 17870,
"gene_symbol": "INVS",
"hgvs_c": "c.1825C>T",
"hgvs_p": "p.His609Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001305311.1",
"strand": true,
"transcript": "NM_001318382.2",
"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": 4848,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 17,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NR_134606.2",
"gene_hgnc_id": 17870,
"gene_symbol": "INVS",
"hgvs_c": "n.2952C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_134606.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs139768159",
"effect": "missense_variant",
"frequency_reference_population": 0.0028017347,
"gene_hgnc_id": 17870,
"gene_symbol": "INVS",
"gnomad_exomes_ac": 4167,
"gnomad_exomes_af": 0.0028507,
"gnomad_exomes_homalt": 14,
"gnomad_genomes_ac": 355,
"gnomad_genomes_af": 0.00233163,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 14,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Nephronophthisis|not specified|Infantile nephronophthisis|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.712,
"pos": 100296933,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.051,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_014425.5"
}
]
}