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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: X-72129944-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=72129944&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 72129944,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000609883.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTL5",
"gene_hgnc_id": 29430,
"hgvs_c": "c.1597C>T",
"hgvs_p": "p.Arg533Cys",
"transcript": "ENST00000609883.3",
"protein_id": "ENSP00000476792.1",
"transcript_support_level": 6,
"aa_start": 533,
"aa_end": null,
"aa_length": 569,
"cds_start": 1597,
"cds_end": null,
"cds_length": 1710,
"cdna_start": 1972,
"cdna_end": null,
"cdna_length": 4806,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTL5",
"gene_hgnc_id": 29430,
"hgvs_c": "n.1597C>T",
"hgvs_p": null,
"transcript": "ENST00000479991.1",
"protein_id": "ENSP00000418667.1",
"transcript_support_level": 1,
"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": 4339,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NHSL2",
"gene_hgnc_id": 33737,
"hgvs_c": "c.281-2135G>A",
"hgvs_p": null,
"transcript": "NM_001013627.3",
"protein_id": "NP_001013649.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1225,
"cds_start": -4,
"cds_end": null,
"cds_length": 3678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13633,
"mane_select": "ENST00000633930.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NHSL2",
"gene_hgnc_id": 33737,
"hgvs_c": "c.281-2135G>A",
"hgvs_p": null,
"transcript": "ENST00000633930.2",
"protein_id": "ENSP00000488668.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1225,
"cds_start": -4,
"cds_end": null,
"cds_length": 3678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13633,
"mane_select": "NM_001013627.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTL5",
"gene_hgnc_id": 29430,
"hgvs_c": "c.1597C>T",
"hgvs_p": "p.Arg533Cys",
"transcript": "NM_001024455.4",
"protein_id": "NP_001019626.1",
"transcript_support_level": null,
"aa_start": 533,
"aa_end": null,
"aa_length": 569,
"cds_start": 1597,
"cds_end": null,
"cds_length": 1710,
"cdna_start": 1972,
"cdna_end": null,
"cdna_length": 4353,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RTL5",
"gene_hgnc_id": 29430,
"hgvs_c": "c.1597C>T",
"hgvs_p": "p.Arg533Cys",
"transcript": "NM_001405151.1",
"protein_id": "NP_001392080.1",
"transcript_support_level": null,
"aa_start": 533,
"aa_end": null,
"aa_length": 569,
"cds_start": 1597,
"cds_end": null,
"cds_length": 1710,
"cdna_start": 1972,
"cdna_end": null,
"cdna_length": 4806,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NHSL2",
"gene_hgnc_id": 33737,
"hgvs_c": "c.350-2135G>A",
"hgvs_p": null,
"transcript": "NM_001438805.1",
"protein_id": "NP_001425734.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1248,
"cds_start": -4,
"cds_end": null,
"cds_length": 3747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13702,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NHSL2",
"gene_hgnc_id": 33737,
"hgvs_c": "c.350-4147G>A",
"hgvs_p": null,
"transcript": "NM_001438806.1",
"protein_id": "NP_001425735.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1196,
"cds_start": -4,
"cds_end": null,
"cds_length": 3591,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13546,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NHSL2",
"gene_hgnc_id": 33737,
"hgvs_c": "c.350-8497G>A",
"hgvs_p": null,
"transcript": "NM_001438807.1",
"protein_id": "NP_001425736.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1044,
"cds_start": -4,
"cds_end": null,
"cds_length": 3135,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13090,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NHSL2",
"gene_hgnc_id": 33737,
"hgvs_c": "c.-281-2135G>A",
"hgvs_p": null,
"transcript": "NM_001438808.1",
"protein_id": "NP_001425737.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1038,
"cds_start": -4,
"cds_end": null,
"cds_length": 3117,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13294,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NHSL2",
"gene_hgnc_id": 33737,
"hgvs_c": "c.68-8497G>A",
"hgvs_p": null,
"transcript": "NM_001438809.1",
"protein_id": "NP_001425738.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 950,
"cds_start": -4,
"cds_end": null,
"cds_length": 2853,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13099,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NHSL2",
"gene_hgnc_id": 33737,
"hgvs_c": "c.68-8497G>A",
"hgvs_p": null,
"transcript": "ENST00000631375.1",
"protein_id": "ENSP00000488715.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 950,
"cds_start": -4,
"cds_end": null,
"cds_length": 2853,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12593,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NHSL2",
"gene_hgnc_id": 33737,
"hgvs_c": "c.44-8497G>A",
"hgvs_p": null,
"transcript": "ENST00000632230.1",
"protein_id": "ENSP00000487835.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 834,
"cds_start": -4,
"cds_end": null,
"cds_length": 2507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2955,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NHSL2",
"gene_hgnc_id": 33737,
"hgvs_c": "n.220-2135G>A",
"hgvs_p": null,
"transcript": "ENST00000631833.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NHSL2",
"gene_hgnc_id": 33737,
"hgvs_c": "c.350-2135G>A",
"hgvs_p": null,
"transcript": "XM_047442065.1",
"protein_id": "XP_047298021.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1204,
"cds_start": -4,
"cds_end": null,
"cds_length": 3615,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NHSL2",
"gene_hgnc_id": 33737,
"hgvs_c": "c.68-2135G>A",
"hgvs_p": null,
"transcript": "XM_047442067.1",
"protein_id": "XP_047298023.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1154,
"cds_start": -4,
"cds_end": null,
"cds_length": 3465,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13711,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NHSL2",
"gene_hgnc_id": 33737,
"hgvs_c": "c.350-4147G>A",
"hgvs_p": null,
"transcript": "XM_047442068.1",
"protein_id": "XP_047298024.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1152,
"cds_start": -4,
"cds_end": null,
"cds_length": 3459,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13414,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NHSL2",
"gene_hgnc_id": 33737,
"hgvs_c": "c.68-4147G>A",
"hgvs_p": null,
"transcript": "XM_047442069.1",
"protein_id": "XP_047298025.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1102,
"cds_start": -4,
"cds_end": null,
"cds_length": 3309,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13555,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NHSL2",
"gene_hgnc_id": 33737,
"hgvs_c": "c.350-2135G>A",
"hgvs_p": null,
"transcript": "XM_011530932.2",
"protein_id": "XP_011529234.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1098,
"cds_start": -4,
"cds_end": null,
"cds_length": 3297,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3540,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NHSL2",
"gene_hgnc_id": 33737,
"hgvs_c": "c.350-2135G>A",
"hgvs_p": null,
"transcript": "XM_011530933.2",
"protein_id": "XP_011529235.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1054,
"cds_start": -4,
"cds_end": null,
"cds_length": 3165,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3994,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RTL5",
"gene_hgnc_id": 29430,
"dbsnp": "rs752851219",
"frequency_reference_population": 0.000007441479,
"hom_count_reference_population": 2,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.0000027327,
"gnomad_genomes_af": 0.0000537533,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.23240801692008972,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.129,
"revel_prediction": "Benign",
"alphamissense_score": 0.1417,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.26,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.657,
"phylop100way_prediction": "Benign",
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000609883.3",
"gene_symbol": "RTL5",
"hgnc_id": 29430,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1597C>T",
"hgvs_p": "p.Arg533Cys"
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_001013627.3",
"gene_symbol": "NHSL2",
"hgnc_id": 33737,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.281-2135G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}