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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: 15-28130164-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=28130164&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 28130164,
"ref": "A",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_004667.6",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 83,
"exon_rank_end": null,
"exon_count": 93,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERC2",
"gene_hgnc_id": 4868,
"hgvs_c": "c.12801T>A",
"hgvs_p": "p.Asp4267Glu",
"transcript": "NM_004667.6",
"protein_id": "NP_004658.3",
"transcript_support_level": null,
"aa_start": 4267,
"aa_end": null,
"aa_length": 4834,
"cds_start": 12801,
"cds_end": null,
"cds_length": 14505,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000261609.13",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004667.6"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 83,
"exon_rank_end": null,
"exon_count": 93,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERC2",
"gene_hgnc_id": 4868,
"hgvs_c": "c.12801T>A",
"hgvs_p": "p.Asp4267Glu",
"transcript": "ENST00000261609.13",
"protein_id": "ENSP00000261609.8",
"transcript_support_level": 1,
"aa_start": 4267,
"aa_end": null,
"aa_length": 4834,
"cds_start": 12801,
"cds_end": null,
"cds_length": 14505,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004667.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000261609.13"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 83,
"exon_rank_end": null,
"exon_count": 93,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERC2",
"gene_hgnc_id": 4868,
"hgvs_c": "c.12786T>A",
"hgvs_p": "p.Asp4262Glu",
"transcript": "XM_006720726.4",
"protein_id": "XP_006720789.1",
"transcript_support_level": null,
"aa_start": 4262,
"aa_end": null,
"aa_length": 4829,
"cds_start": 12786,
"cds_end": null,
"cds_length": 14490,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006720726.4"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 82,
"exon_rank_end": null,
"exon_count": 92,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERC2",
"gene_hgnc_id": 4868,
"hgvs_c": "c.12774T>A",
"hgvs_p": "p.Asp4258Glu",
"transcript": "XM_047433206.1",
"protein_id": "XP_047289162.1",
"transcript_support_level": null,
"aa_start": 4258,
"aa_end": null,
"aa_length": 4825,
"cds_start": 12774,
"cds_end": null,
"cds_length": 14478,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047433206.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 82,
"exon_rank_end": null,
"exon_count": 92,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERC2",
"gene_hgnc_id": 4868,
"hgvs_c": "c.12687T>A",
"hgvs_p": "p.Asp4229Glu",
"transcript": "XM_005268276.6",
"protein_id": "XP_005268333.1",
"transcript_support_level": null,
"aa_start": 4229,
"aa_end": null,
"aa_length": 4796,
"cds_start": 12687,
"cds_end": null,
"cds_length": 14391,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005268276.6"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 82,
"exon_rank_end": null,
"exon_count": 92,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERC2",
"gene_hgnc_id": 4868,
"hgvs_c": "c.12687T>A",
"hgvs_p": "p.Asp4229Glu",
"transcript": "XM_017022695.1",
"protein_id": "XP_016878184.1",
"transcript_support_level": null,
"aa_start": 4229,
"aa_end": null,
"aa_length": 4796,
"cds_start": 12687,
"cds_end": null,
"cds_length": 14391,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017022695.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 82,
"exon_rank_end": null,
"exon_count": 92,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERC2",
"gene_hgnc_id": 4868,
"hgvs_c": "c.12687T>A",
"hgvs_p": "p.Asp4229Glu",
"transcript": "XM_017022696.2",
"protein_id": "XP_016878185.1",
"transcript_support_level": null,
"aa_start": 4229,
"aa_end": null,
"aa_length": 4796,
"cds_start": 12687,
"cds_end": null,
"cds_length": 14391,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017022696.2"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 81,
"exon_rank_end": null,
"exon_count": 91,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERC2",
"gene_hgnc_id": 4868,
"hgvs_c": "c.12543T>A",
"hgvs_p": "p.Asp4181Glu",
"transcript": "XM_006720727.4",
"protein_id": "XP_006720790.1",
"transcript_support_level": null,
"aa_start": 4181,
"aa_end": null,
"aa_length": 4748,
"cds_start": 12543,
"cds_end": null,
"cds_length": 14247,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006720727.4"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 79,
"exon_rank_end": null,
"exon_count": 89,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERC2",
"gene_hgnc_id": 4868,
"hgvs_c": "c.12318T>A",
"hgvs_p": "p.Asp4106Glu",
"transcript": "XM_047433207.1",
"protein_id": "XP_047289163.1",
"transcript_support_level": null,
"aa_start": 4106,
"aa_end": null,
"aa_length": 4673,
"cds_start": 12318,
"cds_end": null,
"cds_length": 14022,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047433207.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERC2",
"gene_hgnc_id": 4868,
"hgvs_c": "c.5967T>A",
"hgvs_p": "p.Asp1989Glu",
"transcript": "XM_017022697.2",
"protein_id": "XP_016878186.1",
"transcript_support_level": null,
"aa_start": 1989,
"aa_end": null,
"aa_length": 2556,
"cds_start": 5967,
"cds_end": null,
"cds_length": 7671,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017022697.2"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERC2",
"gene_hgnc_id": 4868,
"hgvs_c": "c.5967T>A",
"hgvs_p": "p.Asp1989Glu",
"transcript": "XM_017022698.2",
"protein_id": "XP_016878187.1",
"transcript_support_level": null,
"aa_start": 1989,
"aa_end": null,
"aa_length": 2556,
"cds_start": 5967,
"cds_end": null,
"cds_length": 7671,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017022698.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": 29,
"intron_rank_end": null,
"gene_symbol": "HERC2",
"gene_hgnc_id": 4868,
"hgvs_c": "n.4281+1936T>A",
"hgvs_p": null,
"transcript": "ENST00000650509.1",
"protein_id": "ENSP00000496936.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000650509.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERC2",
"gene_hgnc_id": 4868,
"hgvs_c": "n.*136T>A",
"hgvs_p": null,
"transcript": "ENST00000649023.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000649023.1"
}
],
"gene_symbol": "HERC2",
"gene_hgnc_id": 4868,
"dbsnp": "rs373175587",
"frequency_reference_population": 0.00089719327,
"hom_count_reference_population": 23,
"allele_count_reference_population": 1448,
"gnomad_exomes_af": 0.000912531,
"gnomad_genomes_af": 0.000749734,
"gnomad_exomes_ac": 1334,
"gnomad_genomes_ac": 114,
"gnomad_exomes_homalt": 21,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.015111774206161499,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.18199999630451202,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.318,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0748,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.33,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.044,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000326579991845859,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_004667.6",
"gene_symbol": "HERC2",
"hgnc_id": 4868,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.12801T>A",
"hgvs_p": "p.Asp4267Glu"
}
],
"clinvar_disease": "Developmental delay with autism spectrum disorder and gait instability,Inborn genetic diseases,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "not specified|Developmental delay with autism spectrum disorder and gait instability|Inborn genetic diseases|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}