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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: 1-21879030-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=21879030&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 21879030,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000374695.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2435G>A",
"hgvs_p": "p.Arg812Gln",
"transcript": "NM_005529.7",
"protein_id": "NP_005520.4",
"transcript_support_level": null,
"aa_start": 812,
"aa_end": null,
"aa_length": 4391,
"cds_start": 2435,
"cds_end": null,
"cds_length": 13176,
"cdna_start": 2528,
"cdna_end": null,
"cdna_length": 14341,
"mane_select": "ENST00000374695.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2435G>A",
"hgvs_p": "p.Arg812Gln",
"transcript": "ENST00000374695.8",
"protein_id": "ENSP00000363827.3",
"transcript_support_level": 1,
"aa_start": 812,
"aa_end": null,
"aa_length": 4391,
"cds_start": 2435,
"cds_end": null,
"cds_length": 13176,
"cdna_start": 2528,
"cdna_end": null,
"cdna_length": 14341,
"mane_select": "NM_005529.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2438G>A",
"hgvs_p": "p.Arg813Gln",
"transcript": "NM_001291860.2",
"protein_id": "NP_001278789.1",
"transcript_support_level": null,
"aa_start": 813,
"aa_end": null,
"aa_length": 4392,
"cds_start": 2438,
"cds_end": null,
"cds_length": 13179,
"cdna_start": 2531,
"cdna_end": null,
"cdna_length": 14344,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 102,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2489G>A",
"hgvs_p": "p.Arg830Gln",
"transcript": "XM_011541318.3",
"protein_id": "XP_011539620.1",
"transcript_support_level": null,
"aa_start": 830,
"aa_end": null,
"aa_length": 4574,
"cds_start": 2489,
"cds_end": null,
"cds_length": 13725,
"cdna_start": 2582,
"cdna_end": null,
"cdna_length": 14890,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 101,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2438G>A",
"hgvs_p": "p.Arg813Gln",
"transcript": "XM_047419080.1",
"protein_id": "XP_047275036.1",
"transcript_support_level": null,
"aa_start": 813,
"aa_end": null,
"aa_length": 4557,
"cds_start": 2438,
"cds_end": null,
"cds_length": 13674,
"cdna_start": 2531,
"cdna_end": null,
"cdna_length": 14839,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 101,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2435G>A",
"hgvs_p": "p.Arg812Gln",
"transcript": "XM_047419090.1",
"protein_id": "XP_047275046.1",
"transcript_support_level": null,
"aa_start": 812,
"aa_end": null,
"aa_length": 4556,
"cds_start": 2435,
"cds_end": null,
"cds_length": 13671,
"cdna_start": 2528,
"cdna_end": null,
"cdna_length": 14836,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 98,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2630G>A",
"hgvs_p": "p.Arg877Gln",
"transcript": "XM_017001120.1",
"protein_id": "XP_016856609.1",
"transcript_support_level": null,
"aa_start": 877,
"aa_end": null,
"aa_length": 4456,
"cds_start": 2630,
"cds_end": null,
"cds_length": 13371,
"cdna_start": 2645,
"cdna_end": null,
"cdna_length": 14458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 98,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2627G>A",
"hgvs_p": "p.Arg876Gln",
"transcript": "XM_047419091.1",
"protein_id": "XP_047275047.1",
"transcript_support_level": null,
"aa_start": 876,
"aa_end": null,
"aa_length": 4455,
"cds_start": 2627,
"cds_end": null,
"cds_length": 13368,
"cdna_start": 2642,
"cdna_end": null,
"cdna_length": 14455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2579G>A",
"hgvs_p": "p.Arg860Gln",
"transcript": "XM_017001121.1",
"protein_id": "XP_016856610.1",
"transcript_support_level": null,
"aa_start": 860,
"aa_end": null,
"aa_length": 4439,
"cds_start": 2579,
"cds_end": null,
"cds_length": 13320,
"cdna_start": 2594,
"cdna_end": null,
"cdna_length": 14407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.2576G>A",
"hgvs_p": "p.Arg859Gln",
"transcript": "XM_017001122.1",
"protein_id": "XP_016856611.1",
"transcript_support_level": null,
"aa_start": 859,
"aa_end": null,
"aa_length": 4438,
"cds_start": 2576,
"cds_end": null,
"cds_length": 13317,
"cdna_start": 2591,
"cdna_end": null,
"cdna_length": 14404,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "n.45G>A",
"hgvs_p": null,
"transcript": "ENST00000480900.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 500,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"dbsnp": "rs150650673",
"frequency_reference_population": 0.00017966023,
"hom_count_reference_population": 0,
"allele_count_reference_population": 290,
"gnomad_exomes_af": 0.000186068,
"gnomad_genomes_af": 0.000118168,
"gnomad_exomes_ac": 272,
"gnomad_genomes_ac": 18,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.34554678201675415,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.172,
"revel_prediction": "Benign",
"alphamissense_score": 0.1022,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.28,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.117,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "ENST00000374695.8",
"gene_symbol": "HSPG2",
"hgnc_id": 5273,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2435G>A",
"hgvs_p": "p.Arg812Gln"
}
],
"clinvar_disease": "Inborn genetic diseases,Lethal Kniest-like syndrome,Schwartz-Jampel syndrome,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:6",
"phenotype_combined": "not provided|Schwartz-Jampel syndrome|Inborn genetic diseases|Lethal Kniest-like syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}