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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: 1-21855388-GC-TA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=21855388&ref=GC&alt=TA&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [],
"effects": [
"missense_variant"
],
"gene_symbol": "HSPG2",
"hgnc_id": 5273,
"hgvs_c": "c.5915_5916delGCinsTA",
"hgvs_p": "p.Arg1972Leu",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": 0,
"transcript": "NM_001291860.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_score": 0,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "TA",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "1",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 4391,
"aa_ref": "R",
"aa_start": 1971,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14341,
"cdna_start": 6006,
"cds_end": null,
"cds_length": 13176,
"cds_start": 5912,
"consequences": [
"missense_variant"
],
"exon_count": 97,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_005529.7",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.5912_5913delGCinsTA",
"hgvs_p": "p.Arg1971Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000374695.8",
"protein_coding": true,
"protein_id": "NP_005520.4",
"strand": false,
"transcript": "NM_005529.7",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 4391,
"aa_ref": "R",
"aa_start": 1971,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 14341,
"cdna_start": 6006,
"cds_end": null,
"cds_length": 13176,
"cds_start": 5912,
"consequences": [
"missense_variant"
],
"exon_count": 97,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000374695.8",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.5912_5913delGCinsTA",
"hgvs_p": "p.Arg1971Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005529.7",
"protein_coding": true,
"protein_id": "ENSP00000363827.3",
"strand": false,
"transcript": "ENST00000374695.8",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 4392,
"aa_ref": "R",
"aa_start": 1972,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14344,
"cdna_start": 6009,
"cds_end": null,
"cds_length": 13179,
"cds_start": 5915,
"consequences": [
"missense_variant"
],
"exon_count": 97,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001291860.2",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.5915_5916delGCinsTA",
"hgvs_p": "p.Arg1972Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001278789.1",
"strand": false,
"transcript": "NM_001291860.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 4574,
"aa_ref": "R",
"aa_start": 2154,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14890,
"cdna_start": 6555,
"cds_end": null,
"cds_length": 13725,
"cds_start": 6461,
"consequences": [
"missense_variant"
],
"exon_count": 102,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011541318.3",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.6461_6462delGCinsTA",
"hgvs_p": "p.Arg2154Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011539620.1",
"strand": false,
"transcript": "XM_011541318.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 4557,
"aa_ref": "R",
"aa_start": 2137,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14839,
"cdna_start": 6504,
"cds_end": null,
"cds_length": 13674,
"cds_start": 6410,
"consequences": [
"missense_variant"
],
"exon_count": 101,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047419080.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.6410_6411delGCinsTA",
"hgvs_p": "p.Arg2137Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275036.1",
"strand": false,
"transcript": "XM_047419080.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 4556,
"aa_ref": "R",
"aa_start": 2136,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14836,
"cdna_start": 6501,
"cds_end": null,
"cds_length": 13671,
"cds_start": 6407,
"consequences": [
"missense_variant"
],
"exon_count": 101,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047419090.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.6407_6408delGCinsTA",
"hgvs_p": "p.Arg2136Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275046.1",
"strand": false,
"transcript": "XM_047419090.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 4456,
"aa_ref": "R",
"aa_start": 2036,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14458,
"cdna_start": 6123,
"cds_end": null,
"cds_length": 13371,
"cds_start": 6107,
"consequences": [
"missense_variant"
],
"exon_count": 98,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017001120.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.6107_6108delGCinsTA",
"hgvs_p": "p.Arg2036Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016856609.1",
"strand": false,
"transcript": "XM_017001120.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 4455,
"aa_ref": "R",
"aa_start": 2035,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14455,
"cdna_start": 6120,
"cds_end": null,
"cds_length": 13368,
"cds_start": 6104,
"consequences": [
"missense_variant"
],
"exon_count": 98,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047419091.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.6104_6105delGCinsTA",
"hgvs_p": "p.Arg2035Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275047.1",
"strand": false,
"transcript": "XM_047419091.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 4439,
"aa_ref": "R",
"aa_start": 2019,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14407,
"cdna_start": 6072,
"cds_end": null,
"cds_length": 13320,
"cds_start": 6056,
"consequences": [
"missense_variant"
],
"exon_count": 97,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017001121.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.6056_6057delGCinsTA",
"hgvs_p": "p.Arg2019Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016856610.1",
"strand": false,
"transcript": "XM_017001121.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 4438,
"aa_ref": "R",
"aa_start": 2018,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14404,
"cdna_start": 6069,
"cds_end": null,
"cds_length": 13317,
"cds_start": 6053,
"consequences": [
"missense_variant"
],
"exon_count": 97,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017001122.1",
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"hgvs_c": "c.6053_6054delGCinsTA",
"hgvs_p": "p.Arg2018Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016856611.1",
"strand": false,
"transcript": "XM_017001122.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": null,
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 5273,
"gene_symbol": "HSPG2",
"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": "Benign",
"phylop100way_score": 1.738,
"pos": 21855388,
"ref": "GC",
"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_001291860.2"
}
]
}