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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: 3-33051989-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=33051989&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 33051989,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000307363.10",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "c.808T>G",
"hgvs_p": "p.Tyr270Asp",
"transcript": "NM_000404.4",
"protein_id": "NP_000395.3",
"transcript_support_level": null,
"aa_start": 270,
"aa_end": null,
"aa_length": 677,
"cds_start": 808,
"cds_end": null,
"cds_length": 2034,
"cdna_start": 869,
"cdna_end": null,
"cdna_length": 2523,
"mane_select": "ENST00000307363.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "c.808T>G",
"hgvs_p": "p.Tyr270Asp",
"transcript": "ENST00000307363.10",
"protein_id": "ENSP00000306920.4",
"transcript_support_level": 1,
"aa_start": 270,
"aa_end": null,
"aa_length": 677,
"cds_start": 808,
"cds_end": null,
"cds_length": 2034,
"cdna_start": 869,
"cdna_end": null,
"cdna_length": 2523,
"mane_select": "NM_000404.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "c.415T>G",
"hgvs_p": "p.Tyr139Asp",
"transcript": "ENST00000307377.12",
"protein_id": "ENSP00000305920.8",
"transcript_support_level": 1,
"aa_start": 139,
"aa_end": null,
"aa_length": 546,
"cds_start": 415,
"cds_end": null,
"cds_length": 1641,
"cdna_start": 476,
"cdna_end": null,
"cdna_length": 2018,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "c.952T>G",
"hgvs_p": "p.Tyr318Asp",
"transcript": "NM_001317040.2",
"protein_id": "NP_001303969.2",
"transcript_support_level": null,
"aa_start": 318,
"aa_end": null,
"aa_length": 725,
"cds_start": 952,
"cds_end": null,
"cds_length": 2178,
"cdna_start": 1013,
"cdna_end": null,
"cdna_length": 2667,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "c.718T>G",
"hgvs_p": "p.Tyr240Asp",
"transcript": "NM_001079811.3",
"protein_id": "NP_001073279.2",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 647,
"cds_start": 718,
"cds_end": null,
"cds_length": 1944,
"cdna_start": 837,
"cdna_end": null,
"cdna_length": 2491,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "c.718T>G",
"hgvs_p": "p.Tyr240Asp",
"transcript": "ENST00000399402.7",
"protein_id": "ENSP00000382333.2",
"transcript_support_level": 2,
"aa_start": 240,
"aa_end": null,
"aa_length": 647,
"cds_start": 718,
"cds_end": null,
"cds_length": 1944,
"cdna_start": 850,
"cdna_end": null,
"cdna_length": 2512,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "c.808T>G",
"hgvs_p": "p.Tyr270Asp",
"transcript": "NM_001393580.1",
"protein_id": "NP_001380509.1",
"transcript_support_level": null,
"aa_start": 270,
"aa_end": null,
"aa_length": 588,
"cds_start": 808,
"cds_end": null,
"cds_length": 1767,
"cdna_start": 869,
"cdna_end": null,
"cdna_length": 2309,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "c.415T>G",
"hgvs_p": "p.Tyr139Asp",
"transcript": "NM_001135602.3",
"protein_id": "NP_001129074.2",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 546,
"cds_start": 415,
"cds_end": null,
"cds_length": 1641,
"cdna_start": 476,
"cdna_end": null,
"cdna_length": 2130,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "c.331T>G",
"hgvs_p": "p.Tyr111Asp",
"transcript": "ENST00000415454.1",
"protein_id": "ENSP00000411813.1",
"transcript_support_level": 4,
"aa_start": 111,
"aa_end": null,
"aa_length": 184,
"cds_start": 331,
"cds_end": null,
"cds_length": 555,
"cdna_start": 367,
"cdna_end": null,
"cdna_length": 591,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "n.*300T>G",
"hgvs_p": null,
"transcript": "ENST00000438227.1",
"protein_id": "ENSP00000401250.1",
"transcript_support_level": 4,
"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": 569,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "n.*251T>G",
"hgvs_p": null,
"transcript": "ENST00000446732.5",
"protein_id": "ENSP00000407365.1",
"transcript_support_level": 3,
"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": 631,
"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": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "n.183T>G",
"hgvs_p": null,
"transcript": "ENST00000482097.5",
"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": 547,
"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": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "n.211T>G",
"hgvs_p": null,
"transcript": "ENST00000485698.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 550,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "n.334T>G",
"hgvs_p": null,
"transcript": "ENST00000498537.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "n.*300T>G",
"hgvs_p": null,
"transcript": "ENST00000438227.1",
"protein_id": "ENSP00000401250.1",
"transcript_support_level": 4,
"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": 569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"hgvs_c": "n.*251T>G",
"hgvs_p": null,
"transcript": "ENST00000446732.5",
"protein_id": "ENSP00000407365.1",
"transcript_support_level": 3,
"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": 631,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GLB1",
"gene_hgnc_id": 4298,
"dbsnp": "rs376663785",
"frequency_reference_population": 0.000018586232,
"hom_count_reference_population": 0,
"allele_count_reference_population": 30,
"gnomad_exomes_af": 0.0000198376,
"gnomad_genomes_af": 0.00000656901,
"gnomad_exomes_ac": 29,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9656906127929688,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.992,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9016,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.6,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.931,
"phylop100way_prediction": "Pathogenic",
"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": 19,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 19,
"benign_score": 0,
"pathogenic_score": 19,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000307363.10",
"gene_symbol": "GLB1",
"hgnc_id": 4298,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.808T>G",
"hgvs_p": "p.Tyr270Asp"
}
],
"clinvar_disease": " MPS-IV-B,GLB1-related disorder,GM1 gangliosidosis,GM1 gangliosidosis type 2,GM1 gangliosidosis type 3,Inborn genetic diseases,Infantile GM1 gangliosidosis,Mucopolysaccharidosis,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:7 LP:1 O:1",
"phenotype_combined": "not provided|Inborn genetic diseases|Mucopolysaccharidosis, MPS-IV-B;GM1 gangliosidosis|GM1 gangliosidosis type 2;Mucopolysaccharidosis, MPS-IV-B;GM1 gangliosidosis type 3;Infantile GM1 gangliosidosis|Mucopolysaccharidosis, MPS-IV-B|GLB1-related disorder",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}