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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: 5-13777273-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=13777273&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PP3",
"BP6"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DNAH5",
"hgnc_id": 2950,
"hgvs_c": "c.9034A>T",
"hgvs_p": "p.Ile3012Phe",
"inheritance_mode": "AD,AR",
"pathogenic_score": 1,
"score": 0,
"transcript": "NM_001369.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3,BP6",
"acmg_score": 0,
"allele_count_reference_population": 151,
"alphamissense_prediction": "Uncertain_significance",
"alphamissense_score": 0.3919,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.24,
"chr": "5",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Primary ciliary dyskinesia",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8328530788421631,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 4624,
"aa_ref": "I",
"aa_start": 3012,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15781,
"cdna_start": 9284,
"cds_end": null,
"cds_length": 13875,
"cds_start": 9034,
"consequences": [
"missense_variant"
],
"exon_count": 79,
"exon_rank": 54,
"exon_rank_end": null,
"feature": "NM_001369.3",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.9034A>T",
"hgvs_p": "p.Ile3012Phe",
"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": "F",
"aa_end": null,
"aa_length": 4624,
"aa_ref": "I",
"aa_start": 3012,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 15781,
"cdna_start": 9284,
"cds_end": null,
"cds_length": 13875,
"cds_start": 9034,
"consequences": [
"missense_variant"
],
"exon_count": 79,
"exon_rank": 54,
"exon_rank_end": null,
"feature": "ENST00000265104.5",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.9034A>T",
"hgvs_p": "p.Ile3012Phe",
"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": "F",
"aa_end": null,
"aa_length": 4609,
"aa_ref": "I",
"aa_start": 2997,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15645,
"cdna_start": 9148,
"cds_end": null,
"cds_length": 13830,
"cds_start": 8989,
"consequences": [
"missense_variant"
],
"exon_count": 79,
"exon_rank": 54,
"exon_rank_end": null,
"feature": "ENST00000681290.1",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.8989A>T",
"hgvs_p": "p.Ile2997Phe",
"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": "F",
"aa_end": null,
"aa_length": 4660,
"aa_ref": "I",
"aa_start": 3048,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15645,
"cdna_start": 9148,
"cds_end": null,
"cds_length": 13983,
"cds_start": 9142,
"consequences": [
"missense_variant"
],
"exon_count": 79,
"exon_rank": 54,
"exon_rank_end": null,
"feature": "XM_005248262.4",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.9142A>T",
"hgvs_p": "p.Ile3048Phe",
"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": "F",
"aa_end": null,
"aa_length": 4544,
"aa_ref": "I",
"aa_start": 2932,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16410,
"cdna_start": 9913,
"cds_end": null,
"cds_length": 13635,
"cds_start": 8794,
"consequences": [
"missense_variant"
],
"exon_count": 79,
"exon_rank": 54,
"exon_rank_end": null,
"feature": "XM_047416886.1",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.8794A>T",
"hgvs_p": "p.Ile2932Phe",
"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": "F",
"aa_end": null,
"aa_length": 4520,
"aa_ref": "I",
"aa_start": 3048,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15225,
"cdna_start": 9148,
"cds_end": null,
"cds_length": 13563,
"cds_start": 9142,
"consequences": [
"missense_variant"
],
"exon_count": 77,
"exon_rank": 54,
"exon_rank_end": null,
"feature": "XM_017009177.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.9142A>T",
"hgvs_p": "p.Ile3048Phe",
"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": "F",
"aa_end": null,
"aa_length": 4295,
"aa_ref": "I",
"aa_start": 2683,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14753,
"cdna_start": 8256,
"cds_end": null,
"cds_length": 12888,
"cds_start": 8047,
"consequences": [
"missense_variant"
],
"exon_count": 73,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "XM_017009179.3",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.8047A>T",
"hgvs_p": "p.Ile2683Phe",
"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": "F",
"aa_end": null,
"aa_length": 4272,
"aa_ref": "I",
"aa_start": 3048,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12932,
"cdna_start": 9148,
"cds_end": null,
"cds_length": 12819,
"cds_start": 9142,
"consequences": [
"missense_variant"
],
"exon_count": 74,
"exon_rank": 54,
"exon_rank_end": null,
"feature": "XM_017009180.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.9142A>T",
"hgvs_p": "p.Ile3048Phe",
"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": "F",
"aa_end": null,
"aa_length": 3960,
"aa_ref": "I",
"aa_start": 3048,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11987,
"cdna_start": 9148,
"cds_end": null,
"cds_length": 11883,
"cds_start": 9142,
"consequences": [
"missense_variant"
],
"exon_count": 69,
"exon_rank": 54,
"exon_rank_end": null,
"feature": "XM_017009181.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.9142A>T",
"hgvs_p": "p.Ile3048Phe",
"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": "F",
"aa_end": null,
"aa_length": 3809,
"aa_ref": "I",
"aa_start": 3048,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11526,
"cdna_start": 9148,
"cds_end": null,
"cds_length": 11430,
"cds_start": 9142,
"consequences": [
"missense_variant"
],
"exon_count": 67,
"exon_rank": 54,
"exon_rank_end": null,
"feature": "XM_017009182.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.9142A>T",
"hgvs_p": "p.Ile3048Phe",
"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": "F",
"aa_end": null,
"aa_length": 3071,
"aa_ref": "I",
"aa_start": 3048,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9297,
"cdna_start": 9148,
"cds_end": null,
"cds_length": 9216,
"cds_start": 9142,
"consequences": [
"missense_variant"
],
"exon_count": 55,
"exon_rank": 54,
"exon_rank_end": null,
"feature": "XM_017009184.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.9142A>T",
"hgvs_p": "p.Ile3048Phe",
"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": "F",
"aa_end": null,
"aa_length": 3023,
"aa_ref": "I",
"aa_start": 1411,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10952,
"cdna_start": 4455,
"cds_end": null,
"cds_length": 9072,
"cds_start": 4231,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "XM_017009185.1",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.4231A>T",
"hgvs_p": "p.Ile1411Phe",
"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": "F",
"aa_end": null,
"aa_length": 2874,
"aa_ref": "I",
"aa_start": 1262,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10383,
"cdna_start": 3886,
"cds_end": null,
"cds_length": 8625,
"cds_start": 3784,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_017009186.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.3784A>T",
"hgvs_p": "p.Ile1262Phe",
"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": "F",
"aa_end": null,
"aa_length": 2653,
"aa_ref": "I",
"aa_start": 1041,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11185,
"cdna_start": 4688,
"cds_end": null,
"cds_length": 7962,
"cds_start": 3121,
"consequences": [
"missense_variant"
],
"exon_count": 45,
"exon_rank": 20,
"exon_rank_end": null,
"feature": "XM_017009188.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.3121A>T",
"hgvs_p": "p.Ile1041Phe",
"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": "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": 53,
"exon_rank_end": null,
"feature": "XR_001742034.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "n.9017A>T",
"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": 53,
"exon_rank_end": null,
"feature": "XR_001742035.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "n.9017A>T",
"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": "rs368476008",
"effect": "missense_variant",
"frequency_reference_population": 0.00009360243,
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"gnomad_exomes_ac": 145,
"gnomad_exomes_af": 0.0000992461,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 6,
"gnomad_genomes_af": 0.0000394239,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Primary ciliary dyskinesia",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.054,
"pos": 13777273,
"ref": "T",
"revel_prediction": "Benign",
"revel_score": 0.282,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.029999999329447746,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.03,
"transcript": "NM_001369.3"
}
]
}