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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: 5-160565804-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=160565804&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 160565804,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_025153.3",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4035A>C",
"hgvs_p": "p.Glu1345Asp",
"transcript": "NM_025153.3",
"protein_id": "NP_079429.2",
"transcript_support_level": null,
"aa_start": 1345,
"aa_end": null,
"aa_length": 1461,
"cds_start": 4035,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 4881,
"cdna_end": null,
"cdna_length": 7565,
"mane_select": "ENST00000327245.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4035A>C",
"hgvs_p": "p.Glu1345Asp",
"transcript": "ENST00000327245.10",
"protein_id": "ENSP00000313600.5",
"transcript_support_level": 1,
"aa_start": 1345,
"aa_end": null,
"aa_length": 1461,
"cds_start": 4035,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 4881,
"cdna_end": null,
"cdna_length": 7565,
"mane_select": "NM_025153.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4035A>C",
"hgvs_p": "p.Glu1345Asp",
"transcript": "NM_001366652.1",
"protein_id": "NP_001353581.1",
"transcript_support_level": null,
"aa_start": 1345,
"aa_end": null,
"aa_length": 1461,
"cds_start": 4035,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 4520,
"cdna_end": null,
"cdna_length": 7204,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4035A>C",
"hgvs_p": "p.Glu1345Asp",
"transcript": "NM_001366655.1",
"protein_id": "NP_001353584.1",
"transcript_support_level": null,
"aa_start": 1345,
"aa_end": null,
"aa_length": 1461,
"cds_start": 4035,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 4697,
"cdna_end": null,
"cdna_length": 7381,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.3999A>C",
"hgvs_p": "p.Glu1333Asp",
"transcript": "NM_001366657.1",
"protein_id": "NP_001353586.1",
"transcript_support_level": null,
"aa_start": 1333,
"aa_end": null,
"aa_length": 1449,
"cds_start": 3999,
"cds_end": null,
"cds_length": 4350,
"cdna_start": 4661,
"cdna_end": null,
"cdna_length": 7345,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.3951A>C",
"hgvs_p": "p.Glu1317Asp",
"transcript": "NM_001410822.1",
"protein_id": "NP_001397751.1",
"transcript_support_level": null,
"aa_start": 1317,
"aa_end": null,
"aa_length": 1433,
"cds_start": 3951,
"cds_end": null,
"cds_length": 4302,
"cdna_start": 4122,
"cdna_end": null,
"cdna_length": 6806,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.3951A>C",
"hgvs_p": "p.Glu1317Asp",
"transcript": "ENST00000642502.1",
"protein_id": "ENSP00000493802.1",
"transcript_support_level": null,
"aa_start": 1317,
"aa_end": null,
"aa_length": 1433,
"cds_start": 3951,
"cds_end": null,
"cds_length": 4302,
"cdna_start": 4116,
"cdna_end": null,
"cdna_length": 6800,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4035A>C",
"hgvs_p": "p.Glu1345Asp",
"transcript": "XM_011534468.3",
"protein_id": "XP_011532770.1",
"transcript_support_level": null,
"aa_start": 1345,
"aa_end": null,
"aa_length": 1461,
"cds_start": 4035,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 4388,
"cdna_end": null,
"cdna_length": 7072,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4035A>C",
"hgvs_p": "p.Glu1345Asp",
"transcript": "XM_011534469.2",
"protein_id": "XP_011532771.1",
"transcript_support_level": null,
"aa_start": 1345,
"aa_end": null,
"aa_length": 1461,
"cds_start": 4035,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 4704,
"cdna_end": null,
"cdna_length": 7388,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4035A>C",
"hgvs_p": "p.Glu1345Asp",
"transcript": "XM_047416994.1",
"protein_id": "XP_047272950.1",
"transcript_support_level": null,
"aa_start": 1345,
"aa_end": null,
"aa_length": 1461,
"cds_start": 4035,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 4514,
"cdna_end": null,
"cdna_length": 7198,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.3999A>C",
"hgvs_p": "p.Glu1333Asp",
"transcript": "XM_017009252.2",
"protein_id": "XP_016864741.1",
"transcript_support_level": null,
"aa_start": 1333,
"aa_end": null,
"aa_length": 1449,
"cds_start": 3999,
"cds_end": null,
"cds_length": 4350,
"cdna_start": 4352,
"cdna_end": null,
"cdna_length": 7036,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.3834A>C",
"hgvs_p": "p.Glu1278Asp",
"transcript": "XM_047416995.1",
"protein_id": "XP_047272951.1",
"transcript_support_level": null,
"aa_start": 1278,
"aa_end": null,
"aa_length": 1394,
"cds_start": 3834,
"cds_end": null,
"cds_length": 4185,
"cdna_start": 4187,
"cdna_end": null,
"cdna_length": 6871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.3750A>C",
"hgvs_p": "p.Glu1250Asp",
"transcript": "XM_047416996.1",
"protein_id": "XP_047272952.1",
"transcript_support_level": null,
"aa_start": 1250,
"aa_end": null,
"aa_length": 1366,
"cds_start": 3750,
"cds_end": null,
"cds_length": 4101,
"cdna_start": 3921,
"cdna_end": null,
"cdna_length": 6605,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "MIR3142HG",
"gene_hgnc_id": 51944,
"hgvs_c": "n.658-34905T>G",
"hgvs_p": null,
"transcript": "ENST00000770454.1",
"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": 914,
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "MIR3142HG",
"gene_hgnc_id": 51944,
"hgvs_c": "n.563-34905T>G",
"hgvs_p": null,
"transcript": "ENST00000770455.1",
"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": 818,
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "MIR3142HG",
"gene_hgnc_id": 51944,
"hgvs_c": "n.340+13211T>G",
"hgvs_p": null,
"transcript": "ENST00000770456.1",
"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": 594,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "MIR3142HG",
"gene_hgnc_id": 51944,
"hgvs_c": "n.317+13211T>G",
"hgvs_p": null,
"transcript": "ENST00000770457.1",
"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": 574,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"dbsnp": "rs926155295",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.12182176113128662,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.046,
"revel_prediction": "Benign",
"alphamissense_score": 0.2618,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.69,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.421,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_025153.3",
"gene_symbol": "ATP10B",
"hgnc_id": 13543,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4035A>C",
"hgvs_p": "p.Glu1345Asp"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000770454.1",
"gene_symbol": "MIR3142HG",
"hgnc_id": 51944,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.658-34905T>G",
"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
}