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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: 5-13817617-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=13817617&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DNAH5",
"hgnc_id": 2950,
"hgvs_c": "c.6919G>A",
"hgvs_p": "p.Val2307Ile",
"inheritance_mode": "AD,AR",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_001369.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_score": -20,
"allele_count_reference_population": 2121,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1382,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.43,
"chr": "5",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": "Primary ciliary dyskinesia,Primary ciliary dyskinesia 3,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.009432762861251831,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4624,
"aa_ref": "V",
"aa_start": 2307,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15781,
"cdna_start": 7169,
"cds_end": null,
"cds_length": 13875,
"cds_start": 6919,
"consequences": [
"missense_variant"
],
"exon_count": 79,
"exon_rank": 42,
"exon_rank_end": null,
"feature": "NM_001369.3",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.6919G>A",
"hgvs_p": "p.Val2307Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000265104.5",
"protein_coding": true,
"protein_id": "NP_001360.1",
"strand": false,
"transcript": "NM_001369.3",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4624,
"aa_ref": "V",
"aa_start": 2307,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 15781,
"cdna_start": 7169,
"cds_end": null,
"cds_length": 13875,
"cds_start": 6919,
"consequences": [
"missense_variant"
],
"exon_count": 79,
"exon_rank": 42,
"exon_rank_end": null,
"feature": "ENST00000265104.5",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.6919G>A",
"hgvs_p": "p.Val2307Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001369.3",
"protein_coding": true,
"protein_id": "ENSP00000265104.4",
"strand": false,
"transcript": "ENST00000265104.5",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4609,
"aa_ref": "V",
"aa_start": 2292,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15645,
"cdna_start": 7033,
"cds_end": null,
"cds_length": 13830,
"cds_start": 6874,
"consequences": [
"missense_variant"
],
"exon_count": 79,
"exon_rank": 42,
"exon_rank_end": null,
"feature": "ENST00000681290.1",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.6874G>A",
"hgvs_p": "p.Val2292Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000505288.1",
"strand": false,
"transcript": "ENST00000681290.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4660,
"aa_ref": "V",
"aa_start": 2343,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15645,
"cdna_start": 7033,
"cds_end": null,
"cds_length": 13983,
"cds_start": 7027,
"consequences": [
"missense_variant"
],
"exon_count": 79,
"exon_rank": 42,
"exon_rank_end": null,
"feature": "XM_005248262.4",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.7027G>A",
"hgvs_p": "p.Val2343Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005248319.2",
"strand": false,
"transcript": "XM_005248262.4",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4544,
"aa_ref": "V",
"aa_start": 2227,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16410,
"cdna_start": 7798,
"cds_end": null,
"cds_length": 13635,
"cds_start": 6679,
"consequences": [
"missense_variant"
],
"exon_count": 79,
"exon_rank": 42,
"exon_rank_end": null,
"feature": "XM_047416886.1",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.6679G>A",
"hgvs_p": "p.Val2227Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047272842.1",
"strand": false,
"transcript": "XM_047416886.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4520,
"aa_ref": "V",
"aa_start": 2343,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15225,
"cdna_start": 7033,
"cds_end": null,
"cds_length": 13563,
"cds_start": 7027,
"consequences": [
"missense_variant"
],
"exon_count": 77,
"exon_rank": 42,
"exon_rank_end": null,
"feature": "XM_017009177.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.7027G>A",
"hgvs_p": "p.Val2343Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864666.1",
"strand": false,
"transcript": "XM_017009177.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4295,
"aa_ref": "V",
"aa_start": 1978,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14753,
"cdna_start": 6141,
"cds_end": null,
"cds_length": 12888,
"cds_start": 5932,
"consequences": [
"missense_variant"
],
"exon_count": 73,
"exon_rank": 36,
"exon_rank_end": null,
"feature": "XM_017009179.3",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.5932G>A",
"hgvs_p": "p.Val1978Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864668.1",
"strand": false,
"transcript": "XM_017009179.3",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 4272,
"aa_ref": "V",
"aa_start": 2343,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12932,
"cdna_start": 7033,
"cds_end": null,
"cds_length": 12819,
"cds_start": 7027,
"consequences": [
"missense_variant"
],
"exon_count": 74,
"exon_rank": 42,
"exon_rank_end": null,
"feature": "XM_017009180.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.7027G>A",
"hgvs_p": "p.Val2343Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864669.1",
"strand": false,
"transcript": "XM_017009180.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 3960,
"aa_ref": "V",
"aa_start": 2343,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11987,
"cdna_start": 7033,
"cds_end": null,
"cds_length": 11883,
"cds_start": 7027,
"consequences": [
"missense_variant"
],
"exon_count": 69,
"exon_rank": 42,
"exon_rank_end": null,
"feature": "XM_017009181.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.7027G>A",
"hgvs_p": "p.Val2343Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864670.1",
"strand": false,
"transcript": "XM_017009181.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 3809,
"aa_ref": "V",
"aa_start": 2343,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11526,
"cdna_start": 7033,
"cds_end": null,
"cds_length": 11430,
"cds_start": 7027,
"consequences": [
"missense_variant"
],
"exon_count": 67,
"exon_rank": 42,
"exon_rank_end": null,
"feature": "XM_017009182.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.7027G>A",
"hgvs_p": "p.Val2343Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864671.1",
"strand": false,
"transcript": "XM_017009182.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 3071,
"aa_ref": "V",
"aa_start": 2343,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9297,
"cdna_start": 7033,
"cds_end": null,
"cds_length": 9216,
"cds_start": 7027,
"consequences": [
"missense_variant"
],
"exon_count": 55,
"exon_rank": 42,
"exon_rank_end": null,
"feature": "XM_017009184.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.7027G>A",
"hgvs_p": "p.Val2343Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864673.1",
"strand": false,
"transcript": "XM_017009184.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 3023,
"aa_ref": "V",
"aa_start": 706,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10952,
"cdna_start": 2340,
"cds_end": null,
"cds_length": 9072,
"cds_start": 2116,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "XM_017009185.1",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.2116G>A",
"hgvs_p": "p.Val706Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864674.1",
"strand": false,
"transcript": "XM_017009185.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 2874,
"aa_ref": "V",
"aa_start": 557,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10383,
"cdna_start": 1771,
"cds_end": null,
"cds_length": 8625,
"cds_start": 1669,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_017009186.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.1669G>A",
"hgvs_p": "p.Val557Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864675.1",
"strand": false,
"transcript": "XM_017009186.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 2679,
"aa_ref": "V",
"aa_start": 2343,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8130,
"cdna_start": 7033,
"cds_end": null,
"cds_length": 8040,
"cds_start": 7027,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 42,
"exon_rank_end": null,
"feature": "XM_017009187.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.7027G>A",
"hgvs_p": "p.Val2343Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864676.1",
"strand": false,
"transcript": "XM_017009187.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 2653,
"aa_ref": "V",
"aa_start": 336,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11185,
"cdna_start": 2573,
"cds_end": null,
"cds_length": 7962,
"cds_start": 1006,
"consequences": [
"missense_variant"
],
"exon_count": 45,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_017009188.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.1006G>A",
"hgvs_p": "p.Val336Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864677.1",
"strand": false,
"transcript": "XM_017009188.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1897,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000683090.1",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "n.1850G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000683090.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 9175,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 54,
"exon_rank": 42,
"exon_rank_end": null,
"feature": "XR_001742034.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "n.7033G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_001742034.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 9166,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 54,
"exon_rank": 42,
"exon_rank_end": null,
"feature": "XR_001742035.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "n.7033G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_001742035.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs74604638",
"effect": "missense_variant",
"frequency_reference_population": 0.0013139815,
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"gnomad_exomes_ac": 1004,
"gnomad_exomes_af": 0.000686802,
"gnomad_exomes_homalt": 13,
"gnomad_genomes_ac": 1117,
"gnomad_genomes_af": 0.00733276,
"gnomad_genomes_homalt": 14,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 27,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "not specified|not provided|Primary ciliary dyskinesia|Primary ciliary dyskinesia 3",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.876,
"pos": 13817617,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.149,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001369.3"
}
]
}