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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: 1-21890111-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=21890111&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 21890111,
"ref": "C",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_001291860.2",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.444G>T",
"hgvs_p": "p.Leu148Leu",
"transcript": "NM_005529.7",
"protein_id": "NP_005520.4",
"transcript_support_level": null,
"aa_start": 148,
"aa_end": null,
"aa_length": 4391,
"cds_start": 444,
"cds_end": null,
"cds_length": 13176,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000374695.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005529.7"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.444G>T",
"hgvs_p": "p.Leu148Leu",
"transcript": "ENST00000374695.8",
"protein_id": "ENSP00000363827.3",
"transcript_support_level": 1,
"aa_start": 148,
"aa_end": null,
"aa_length": 4391,
"cds_start": 444,
"cds_end": null,
"cds_length": 13176,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005529.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000374695.8"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.444G>T",
"hgvs_p": "p.Leu148Leu",
"transcript": "NM_001291860.2",
"protein_id": "NP_001278789.1",
"transcript_support_level": null,
"aa_start": 148,
"aa_end": null,
"aa_length": 4392,
"cds_start": 444,
"cds_end": null,
"cds_length": 13179,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001291860.2"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.198G>T",
"hgvs_p": "p.Leu66Leu",
"transcript": "ENST00000374673.4",
"protein_id": "ENSP00000497688.1",
"transcript_support_level": 3,
"aa_start": 66,
"aa_end": null,
"aa_length": 286,
"cds_start": 198,
"cds_end": null,
"cds_length": 863,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000374673.4"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 102,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.444G>T",
"hgvs_p": "p.Leu148Leu",
"transcript": "XM_011541318.3",
"protein_id": "XP_011539620.1",
"transcript_support_level": null,
"aa_start": 148,
"aa_end": null,
"aa_length": 4574,
"cds_start": 444,
"cds_end": null,
"cds_length": 13725,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541318.3"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 101,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.444G>T",
"hgvs_p": "p.Leu148Leu",
"transcript": "XM_047419080.1",
"protein_id": "XP_047275036.1",
"transcript_support_level": null,
"aa_start": 148,
"aa_end": null,
"aa_length": 4557,
"cds_start": 444,
"cds_end": null,
"cds_length": 13674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047419080.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 101,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.444G>T",
"hgvs_p": "p.Leu148Leu",
"transcript": "XM_047419090.1",
"protein_id": "XP_047275046.1",
"transcript_support_level": null,
"aa_start": 148,
"aa_end": null,
"aa_length": 4556,
"cds_start": 444,
"cds_end": null,
"cds_length": 13671,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047419090.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 98,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.585G>T",
"hgvs_p": "p.Leu195Leu",
"transcript": "XM_017001120.1",
"protein_id": "XP_016856609.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 4456,
"cds_start": 585,
"cds_end": null,
"cds_length": 13371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001120.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 98,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.585G>T",
"hgvs_p": "p.Leu195Leu",
"transcript": "XM_047419091.1",
"protein_id": "XP_047275047.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 4455,
"cds_start": 585,
"cds_end": null,
"cds_length": 13368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047419091.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.585G>T",
"hgvs_p": "p.Leu195Leu",
"transcript": "XM_017001121.1",
"protein_id": "XP_016856610.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 4439,
"cds_start": 585,
"cds_end": null,
"cds_length": 13320,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001121.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 97,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "c.585G>T",
"hgvs_p": "p.Leu195Leu",
"transcript": "XM_017001122.1",
"protein_id": "XP_016856611.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 4438,
"cds_start": 585,
"cds_end": null,
"cds_length": 13317,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001122.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "n.212G>T",
"hgvs_p": null,
"transcript": "ENST00000412328.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000412328.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"hgvs_c": "n.342G>T",
"hgvs_p": null,
"transcript": "ENST00000439717.2",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000439717.2"
}
],
"gene_symbol": "HSPG2",
"gene_hgnc_id": 5273,
"dbsnp": "rs2254357",
"frequency_reference_population": 0.000010534887,
"hom_count_reference_population": 0,
"allele_count_reference_population": 17,
"gnomad_exomes_af": 0.0000102615,
"gnomad_genomes_af": 0.0000131655,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1459999978542328,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.146,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.139,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_001291860.2",
"gene_symbol": "HSPG2",
"hgnc_id": 5273,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.444G>T",
"hgvs_p": "p.Leu148Leu"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}