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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: 4-987873-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=987873&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 987873,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000514224.2",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.223G>A",
"hgvs_p": "p.Ala75Thr",
"transcript": "NM_000203.5",
"protein_id": "NP_000194.2",
"transcript_support_level": null,
"aa_start": 75,
"aa_end": null,
"aa_length": 653,
"cds_start": 223,
"cds_end": null,
"cds_length": 1962,
"cdna_start": 264,
"cdna_end": null,
"cdna_length": 2174,
"mane_select": "ENST00000514224.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.223G>A",
"hgvs_p": "p.Ala75Thr",
"transcript": "ENST00000514224.2",
"protein_id": "ENSP00000425081.2",
"transcript_support_level": 2,
"aa_start": 75,
"aa_end": null,
"aa_length": 653,
"cds_start": 223,
"cds_end": null,
"cds_length": 1962,
"cdna_start": 264,
"cdna_end": null,
"cdna_length": 2174,
"mane_select": "NM_000203.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.223G>A",
"hgvs_p": "p.Ala75Thr",
"transcript": "ENST00000247933.9",
"protein_id": "ENSP00000247933.4",
"transcript_support_level": 1,
"aa_start": 75,
"aa_end": null,
"aa_length": 653,
"cds_start": 223,
"cds_end": null,
"cds_length": 1962,
"cdna_start": 311,
"cdna_end": null,
"cdna_length": 2186,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC26A1",
"gene_hgnc_id": 10993,
"hgvs_c": "c.*960C>T",
"hgvs_p": null,
"transcript": "NM_022042.4",
"protein_id": "NP_071325.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 701,
"cds_start": -4,
"cds_end": null,
"cds_length": 2106,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3413,
"mane_select": "ENST00000398516.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC26A1",
"gene_hgnc_id": 10993,
"hgvs_c": "c.*960C>T",
"hgvs_p": null,
"transcript": "ENST00000398516.3",
"protein_id": "ENSP00000381528.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 701,
"cds_start": -4,
"cds_end": null,
"cds_length": 2106,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3413,
"mane_select": "NM_022042.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC26A1",
"gene_hgnc_id": 10993,
"hgvs_c": "c.*960C>T",
"hgvs_p": null,
"transcript": "ENST00000361661.6",
"protein_id": "ENSP00000354721.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 701,
"cds_start": -4,
"cds_end": null,
"cds_length": 2106,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3660,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC26A1",
"gene_hgnc_id": 10993,
"hgvs_c": "c.576+3255C>T",
"hgvs_p": null,
"transcript": "ENST00000398520.6",
"protein_id": "ENSP00000381532.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 224,
"cds_start": -4,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1111,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.223G>A",
"hgvs_p": "p.Ala75Thr",
"transcript": "XM_047415650.1",
"protein_id": "XP_047271606.1",
"transcript_support_level": null,
"aa_start": 75,
"aa_end": null,
"aa_length": 632,
"cds_start": 223,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 311,
"cdna_end": null,
"cdna_length": 2099,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.219G>A",
"hgvs_p": "p.Ser73Ser",
"transcript": "ENST00000504568.5",
"protein_id": "ENSP00000424847.1",
"transcript_support_level": 3,
"aa_start": 73,
"aa_end": null,
"aa_length": 193,
"cds_start": 219,
"cds_end": null,
"cds_length": 584,
"cdna_start": 221,
"cdna_end": null,
"cdna_length": 586,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "n.232G>A",
"hgvs_p": null,
"transcript": "ENST00000506561.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 692,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "n.311G>A",
"hgvs_p": null,
"transcript": "NR_110313.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2218,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC26A1",
"gene_hgnc_id": 10993,
"hgvs_c": "n.3093C>T",
"hgvs_p": null,
"transcript": "XR_007096347.1",
"protein_id": null,
"transcript_support_level": null,
"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": 4674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC26A1",
"gene_hgnc_id": 10993,
"hgvs_c": "c.*960C>T",
"hgvs_p": null,
"transcript": "NM_213613.4",
"protein_id": "NP_998778.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 701,
"cds_start": -4,
"cds_end": null,
"cds_length": 2106,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC26A1",
"gene_hgnc_id": 10993,
"hgvs_c": "c.576+3255C>T",
"hgvs_p": null,
"transcript": "NM_134425.4",
"protein_id": "NP_602297.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 224,
"cds_start": -4,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1177,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SLC26A1",
"gene_hgnc_id": 10993,
"hgvs_c": "c.576+3255C>T",
"hgvs_p": null,
"transcript": "ENST00000622731.4",
"protein_id": "ENSP00000483506.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 224,
"cds_start": -4,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1057,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "c.158+631G>A",
"hgvs_p": null,
"transcript": "ENST00000502910.5",
"protein_id": "ENSP00000422952.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 223,
"cds_start": -4,
"cds_end": null,
"cds_length": 673,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 714,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "n.177+631G>A",
"hgvs_p": null,
"transcript": "ENST00000508168.5",
"protein_id": null,
"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": 520,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "n.199+631G>A",
"hgvs_p": null,
"transcript": "ENST00000514698.5",
"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": 2185,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"hgvs_c": "n.-42G>A",
"hgvs_p": null,
"transcript": "ENST00000509744.1",
"protein_id": null,
"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": 428,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IDUA",
"gene_hgnc_id": 5391,
"dbsnp": "rs758452450",
"frequency_reference_population": 0.000011787156,
"hom_count_reference_population": 0,
"allele_count_reference_population": 19,
"gnomad_exomes_af": 0.0000123306,
"gnomad_genomes_af": 0.00000657263,
"gnomad_exomes_ac": 18,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9817649722099304,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.803,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.2592,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.28,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.506,
"phylop100way_prediction": "Uncertain_significance",
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3_Supporting,PP4_Moderate,PM2_Supporting,PM3_Strong,PP3_Moderate",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PS3_Supporting",
"PP4_Moderate",
"PM2_Supporting",
"PM3_Strong",
"PP3_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000514224.2",
"gene_symbol": "IDUA",
"hgnc_id": 5391,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.223G>A",
"hgvs_p": "p.Ala75Thr"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000398516.3",
"gene_symbol": "SLC26A1",
"hgnc_id": 10993,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*960C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Hurler syndrome,Mucopolysaccharidosis type 1,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:5",
"phenotype_combined": "Mucopolysaccharidosis type 1|Hurler syndrome|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}