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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: 5-13708287-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=13708287&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 13708287,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000265104.5",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 76,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.13174T>C",
"hgvs_p": "p.Phe4392Leu",
"transcript": "NM_001369.3",
"protein_id": "NP_001360.1",
"transcript_support_level": null,
"aa_start": 4392,
"aa_end": null,
"aa_length": 4624,
"cds_start": 13174,
"cds_end": null,
"cds_length": 13875,
"cdna_start": 13424,
"cdna_end": null,
"cdna_length": 15781,
"mane_select": "ENST00000265104.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 76,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.13174T>C",
"hgvs_p": "p.Phe4392Leu",
"transcript": "ENST00000265104.5",
"protein_id": "ENSP00000265104.4",
"transcript_support_level": 1,
"aa_start": 4392,
"aa_end": null,
"aa_length": 4624,
"cds_start": 13174,
"cds_end": null,
"cds_length": 13875,
"cdna_start": 13424,
"cdna_end": null,
"cdna_length": 15781,
"mane_select": "NM_001369.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 76,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.13129T>C",
"hgvs_p": "p.Phe4377Leu",
"transcript": "ENST00000681290.1",
"protein_id": "ENSP00000505288.1",
"transcript_support_level": null,
"aa_start": 4377,
"aa_end": null,
"aa_length": 4609,
"cds_start": 13129,
"cds_end": null,
"cds_length": 13830,
"cdna_start": 13288,
"cdna_end": null,
"cdna_length": 15645,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 76,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.13282T>C",
"hgvs_p": "p.Phe4428Leu",
"transcript": "XM_005248262.4",
"protein_id": "XP_005248319.2",
"transcript_support_level": null,
"aa_start": 4428,
"aa_end": null,
"aa_length": 4660,
"cds_start": 13282,
"cds_end": null,
"cds_length": 13983,
"cdna_start": 13288,
"cdna_end": null,
"cdna_length": 15645,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 76,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.12934T>C",
"hgvs_p": "p.Phe4312Leu",
"transcript": "XM_047416886.1",
"protein_id": "XP_047272842.1",
"transcript_support_level": null,
"aa_start": 4312,
"aa_end": null,
"aa_length": 4544,
"cds_start": 12934,
"cds_end": null,
"cds_length": 13635,
"cdna_start": 14053,
"cdna_end": null,
"cdna_length": 16410,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 74,
"exon_rank_end": null,
"exon_count": 77,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.12862T>C",
"hgvs_p": "p.Phe4288Leu",
"transcript": "XM_017009177.2",
"protein_id": "XP_016864666.1",
"transcript_support_level": null,
"aa_start": 4288,
"aa_end": null,
"aa_length": 4520,
"cds_start": 12862,
"cds_end": null,
"cds_length": 13563,
"cdna_start": 12868,
"cdna_end": null,
"cdna_length": 15225,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 70,
"exon_rank_end": null,
"exon_count": 73,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.12187T>C",
"hgvs_p": "p.Phe4063Leu",
"transcript": "XM_017009179.3",
"protein_id": "XP_016864668.1",
"transcript_support_level": null,
"aa_start": 4063,
"aa_end": null,
"aa_length": 4295,
"cds_start": 12187,
"cds_end": null,
"cds_length": 12888,
"cdna_start": 12396,
"cdna_end": null,
"cdna_length": 14753,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.8371T>C",
"hgvs_p": "p.Phe2791Leu",
"transcript": "XM_017009185.1",
"protein_id": "XP_016864674.1",
"transcript_support_level": null,
"aa_start": 2791,
"aa_end": null,
"aa_length": 3023,
"cds_start": 8371,
"cds_end": null,
"cds_length": 9072,
"cdna_start": 8595,
"cdna_end": null,
"cdna_length": 10952,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.7924T>C",
"hgvs_p": "p.Phe2642Leu",
"transcript": "XM_017009186.2",
"protein_id": "XP_016864675.1",
"transcript_support_level": null,
"aa_start": 2642,
"aa_end": null,
"aa_length": 2874,
"cds_start": 7924,
"cds_end": null,
"cds_length": 8625,
"cdna_start": 8026,
"cdna_end": null,
"cdna_length": 10383,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "c.7261T>C",
"hgvs_p": "p.Phe2421Leu",
"transcript": "XM_017009188.2",
"protein_id": "XP_016864677.1",
"transcript_support_level": null,
"aa_start": 2421,
"aa_end": null,
"aa_length": 2653,
"cds_start": 7261,
"cds_end": null,
"cds_length": 7962,
"cdna_start": 8828,
"cdna_end": null,
"cdna_length": 11185,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"hgvs_c": "n.507T>C",
"hgvs_p": null,
"transcript": "ENST00000683611.1",
"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": 2844,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DNAH5",
"gene_hgnc_id": 2950,
"dbsnp": "rs369714206",
"frequency_reference_population": 0.000045225097,
"hom_count_reference_population": 0,
"allele_count_reference_population": 73,
"gnomad_exomes_af": 0.0000259941,
"gnomad_genomes_af": 0.000229843,
"gnomad_exomes_ac": 38,
"gnomad_genomes_ac": 35,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7789366245269775,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.372,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9831,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.14,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.271,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3,BP6",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 1,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000265104.5",
"gene_symbol": "DNAH5",
"hgnc_id": 2950,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.13174T>C",
"hgvs_p": "p.Phe4392Leu"
}
],
"clinvar_disease": "Primary ciliary dyskinesia,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "Primary ciliary dyskinesia|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}