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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: 5-13753387-ATAG-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=13753387&ref=ATAG&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 13753387,
"ref": "ATAG",
"alt": "A",
"effect": "disruptive_inframe_deletion",
"transcript": "ENST00000265104.5",
"consequences": [
{
"aa_ref": "TI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.10715_10717delCTA",
"hgvs_p": "p.Thr3572del",
"transcript": "NM_001369.3",
"protein_id": "NP_001360.1",
"transcript_support_level": null,
"aa_start": 3572,
"aa_end": null,
"aa_length": 4624,
"cds_start": 10715,
"cds_end": null,
"cds_length": 13875,
"cdna_start": 10967,
"cdna_end": null,
"cdna_length": 15781,
"mane_select": "ENST00000265104.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "TI",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.10715_10717delCTA",
"hgvs_p": "p.Thr3572del",
"transcript": "ENST00000265104.5",
"protein_id": "ENSP00000265104.4",
"transcript_support_level": 1,
"aa_start": 3572,
"aa_end": null,
"aa_length": 4624,
"cds_start": 10715,
"cds_end": null,
"cds_length": 13875,
"cdna_start": 10967,
"cdna_end": null,
"cdna_length": 15781,
"mane_select": "NM_001369.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "TI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.10670_10672delCTA",
"hgvs_p": "p.Thr3557del",
"transcript": "ENST00000681290.1",
"protein_id": "ENSP00000505288.1",
"transcript_support_level": null,
"aa_start": 3557,
"aa_end": null,
"aa_length": 4609,
"cds_start": 10670,
"cds_end": null,
"cds_length": 13830,
"cdna_start": 10831,
"cdna_end": null,
"cdna_length": 15645,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "TI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.10823_10825delCTA",
"hgvs_p": "p.Thr3608del",
"transcript": "XM_005248262.4",
"protein_id": "XP_005248319.2",
"transcript_support_level": null,
"aa_start": 3608,
"aa_end": null,
"aa_length": 4660,
"cds_start": 10823,
"cds_end": null,
"cds_length": 13983,
"cdna_start": 10831,
"cdna_end": null,
"cdna_length": 15645,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "TI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.10475_10477delCTA",
"hgvs_p": "p.Thr3492del",
"transcript": "XM_047416886.1",
"protein_id": "XP_047272842.1",
"transcript_support_level": null,
"aa_start": 3492,
"aa_end": null,
"aa_length": 4544,
"cds_start": 10475,
"cds_end": null,
"cds_length": 13635,
"cdna_start": 11596,
"cdna_end": null,
"cdna_length": 16410,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "TI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 77,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.10823_10825delCTA",
"hgvs_p": "p.Thr3608del",
"transcript": "XM_017009177.2",
"protein_id": "XP_016864666.1",
"transcript_support_level": null,
"aa_start": 3608,
"aa_end": null,
"aa_length": 4520,
"cds_start": 10823,
"cds_end": null,
"cds_length": 13563,
"cdna_start": 10831,
"cdna_end": null,
"cdna_length": 15225,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "TI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 57,
"exon_rank_end": null,
"exon_count": 73,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.9728_9730delCTA",
"hgvs_p": "p.Thr3243del",
"transcript": "XM_017009179.3",
"protein_id": "XP_016864668.1",
"transcript_support_level": null,
"aa_start": 3243,
"aa_end": null,
"aa_length": 4295,
"cds_start": 9728,
"cds_end": null,
"cds_length": 12888,
"cdna_start": 9939,
"cdna_end": null,
"cdna_length": 14753,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "TI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 74,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.10823_10825delCTA",
"hgvs_p": "p.Thr3608del",
"transcript": "XM_017009180.2",
"protein_id": "XP_016864669.1",
"transcript_support_level": null,
"aa_start": 3608,
"aa_end": null,
"aa_length": 4272,
"cds_start": 10823,
"cds_end": null,
"cds_length": 12819,
"cdna_start": 10831,
"cdna_end": null,
"cdna_length": 12932,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "TI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 69,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.10823_10825delCTA",
"hgvs_p": "p.Thr3608del",
"transcript": "XM_017009181.2",
"protein_id": "XP_016864670.1",
"transcript_support_level": null,
"aa_start": 3608,
"aa_end": null,
"aa_length": 3960,
"cds_start": 10823,
"cds_end": null,
"cds_length": 11883,
"cdna_start": 10831,
"cdna_end": null,
"cdna_length": 11987,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "TI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 63,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.10823_10825delCTA",
"hgvs_p": "p.Thr3608del",
"transcript": "XM_017009182.2",
"protein_id": "XP_016864671.1",
"transcript_support_level": null,
"aa_start": 3608,
"aa_end": null,
"aa_length": 3809,
"cds_start": 10823,
"cds_end": null,
"cds_length": 11430,
"cdna_start": 10831,
"cdna_end": null,
"cdna_length": 11526,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "TI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.5912_5914delCTA",
"hgvs_p": "p.Thr1971del",
"transcript": "XM_017009185.1",
"protein_id": "XP_016864674.1",
"transcript_support_level": null,
"aa_start": 1971,
"aa_end": null,
"aa_length": 3023,
"cds_start": 5912,
"cds_end": null,
"cds_length": 9072,
"cdna_start": 6138,
"cdna_end": null,
"cdna_length": 10952,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "TI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.5465_5467delCTA",
"hgvs_p": "p.Thr1822del",
"transcript": "XM_017009186.2",
"protein_id": "XP_016864675.1",
"transcript_support_level": null,
"aa_start": 1822,
"aa_end": null,
"aa_length": 2874,
"cds_start": 5465,
"cds_end": null,
"cds_length": 8625,
"cdna_start": 5569,
"cdna_end": null,
"cdna_length": 10383,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "TI",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.4802_4804delCTA",
"hgvs_p": "p.Thr1601del",
"transcript": "XM_017009188.2",
"protein_id": "XP_016864677.1",
"transcript_support_level": null,
"aa_start": 1601,
"aa_end": null,
"aa_length": 2653,
"cds_start": 4802,
"cds_end": null,
"cds_length": 7962,
"cdna_start": 6371,
"cdna_end": null,
"cdna_length": 11185,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"dbsnp": "rs773869600",
"frequency_reference_population": 0.00003345845,
"hom_count_reference_population": 0,
"allele_count_reference_population": 54,
"gnomad_exomes_af": 0.0000355731,
"gnomad_genomes_af": 0.0000131439,
"gnomad_exomes_ac": 52,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 7.692,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM4_Supporting",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PM4_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000265104.5",
"gene_symbol": "DNAH5",
"hgnc_id": 2950,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.10715_10717delCTA",
"hgvs_p": "p.Thr3572del"
}
],
"clinvar_disease": "Primary ciliary dyskinesia,Primary ciliary dyskinesia 3",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Primary ciliary dyskinesia|Primary ciliary dyskinesia 3",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}