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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: 5-13700674-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=13700674&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 3,
"criteria": [
"BP4_Moderate",
"BP6"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DNAH5",
"hgnc_id": 2950,
"hgvs_c": "c.13689G>C",
"hgvs_p": "p.Leu4563Phe",
"inheritance_mode": "AD,AR",
"pathogenic_score": 0,
"score": -3,
"transcript": "NM_001369.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BP6",
"acmg_score": -3,
"allele_count_reference_population": 186,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.14,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.6,
"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": "Benign",
"computational_score_selected": 0.21646258234977722,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 4624,
"aa_ref": "L",
"aa_start": 4563,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15781,
"cdna_start": 13939,
"cds_end": null,
"cds_length": 13875,
"cds_start": 13689,
"consequences": [
"missense_variant"
],
"exon_count": 79,
"exon_rank": 78,
"exon_rank_end": null,
"feature": "NM_001369.3",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.13689G>C",
"hgvs_p": "p.Leu4563Phe",
"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": "L",
"aa_start": 4563,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 15781,
"cdna_start": 13939,
"cds_end": null,
"cds_length": 13875,
"cds_start": 13689,
"consequences": [
"missense_variant"
],
"exon_count": 79,
"exon_rank": 78,
"exon_rank_end": null,
"feature": "ENST00000265104.5",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.13689G>C",
"hgvs_p": "p.Leu4563Phe",
"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": "L",
"aa_start": 4548,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15645,
"cdna_start": 13803,
"cds_end": null,
"cds_length": 13830,
"cds_start": 13644,
"consequences": [
"missense_variant"
],
"exon_count": 79,
"exon_rank": 78,
"exon_rank_end": null,
"feature": "ENST00000681290.1",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.13644G>C",
"hgvs_p": "p.Leu4548Phe",
"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": "L",
"aa_start": 4599,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15645,
"cdna_start": 13803,
"cds_end": null,
"cds_length": 13983,
"cds_start": 13797,
"consequences": [
"missense_variant"
],
"exon_count": 79,
"exon_rank": 78,
"exon_rank_end": null,
"feature": "XM_005248262.4",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.13797G>C",
"hgvs_p": "p.Leu4599Phe",
"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": "L",
"aa_start": 4483,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16410,
"cdna_start": 14568,
"cds_end": null,
"cds_length": 13635,
"cds_start": 13449,
"consequences": [
"missense_variant"
],
"exon_count": 79,
"exon_rank": 78,
"exon_rank_end": null,
"feature": "XM_047416886.1",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.13449G>C",
"hgvs_p": "p.Leu4483Phe",
"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": "L",
"aa_start": 4459,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 15225,
"cdna_start": 13383,
"cds_end": null,
"cds_length": 13563,
"cds_start": 13377,
"consequences": [
"missense_variant"
],
"exon_count": 77,
"exon_rank": 76,
"exon_rank_end": null,
"feature": "XM_017009177.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.13377G>C",
"hgvs_p": "p.Leu4459Phe",
"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": "L",
"aa_start": 4234,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 14753,
"cdna_start": 12911,
"cds_end": null,
"cds_length": 12888,
"cds_start": 12702,
"consequences": [
"missense_variant"
],
"exon_count": 73,
"exon_rank": 72,
"exon_rank_end": null,
"feature": "XM_017009179.3",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.12702G>C",
"hgvs_p": "p.Leu4234Phe",
"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": 3023,
"aa_ref": "L",
"aa_start": 2962,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10952,
"cdna_start": 9110,
"cds_end": null,
"cds_length": 9072,
"cds_start": 8886,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 50,
"exon_rank_end": null,
"feature": "XM_017009185.1",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.8886G>C",
"hgvs_p": "p.Leu2962Phe",
"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": "L",
"aa_start": 2813,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10383,
"cdna_start": 8541,
"cds_end": null,
"cds_length": 8625,
"cds_start": 8439,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "XM_017009186.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.8439G>C",
"hgvs_p": "p.Leu2813Phe",
"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": "L",
"aa_start": 2592,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11185,
"cdna_start": 9343,
"cds_end": null,
"cds_length": 7962,
"cds_start": 7776,
"consequences": [
"missense_variant"
],
"exon_count": 45,
"exon_rank": 44,
"exon_rank_end": null,
"feature": "XM_017009188.2",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "c.7776G>C",
"hgvs_p": "p.Leu2592Phe",
"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": 2844,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000683611.1",
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"hgvs_c": "n.1022G>C",
"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": "ENST00000683611.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs374221053",
"effect": "missense_variant",
"frequency_reference_population": 0.000115237206,
"gene_hgnc_id": 2950,
"gene_symbol": "DNAH5",
"gnomad_exomes_ac": 176,
"gnomad_exomes_af": 0.000120394,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 10,
"gnomad_genomes_af": 0.000065703,
"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": 0.109,
"pos": 13700674,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.095,
"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"
}
]
}