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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: 16-56940187-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=56940187&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 56940187,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_014685.4",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.847T>C",
"hgvs_p": "p.Phe283Leu",
"transcript": "NM_014685.4",
"protein_id": "NP_055500.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 391,
"cds_start": 847,
"cds_end": null,
"cds_length": 1176,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000439977.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014685.4"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.847T>C",
"hgvs_p": "p.Phe283Leu",
"transcript": "ENST00000439977.7",
"protein_id": "ENSP00000409555.2",
"transcript_support_level": 1,
"aa_start": 283,
"aa_end": null,
"aa_length": 391,
"cds_start": 847,
"cds_end": null,
"cds_length": 1176,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_014685.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000439977.7"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.844T>C",
"hgvs_p": "p.Phe282Leu",
"transcript": "ENST00000300302.9",
"protein_id": "ENSP00000300302.5",
"transcript_support_level": 1,
"aa_start": 282,
"aa_end": null,
"aa_length": 390,
"cds_start": 844,
"cds_end": null,
"cds_length": 1173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000300302.9"
},
{
"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": 4,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.429-1945T>C",
"hgvs_p": null,
"transcript": "ENST00000344114.8",
"protein_id": "ENSP00000340931.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 232,
"cds_start": null,
"cds_end": null,
"cds_length": 699,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000344114.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "n.1283T>C",
"hgvs_p": null,
"transcript": "ENST00000564678.1",
"protein_id": null,
"transcript_support_level": 1,
"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": "retained_intron",
"feature": "ENST00000564678.1"
},
{
"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": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "n.845+99T>C",
"hgvs_p": null,
"transcript": "ENST00000570273.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000570273.5"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.874T>C",
"hgvs_p": "p.Phe292Leu",
"transcript": "ENST00000855548.1",
"protein_id": "ENSP00000525607.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 400,
"cds_start": 874,
"cds_end": null,
"cds_length": 1203,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855548.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.847T>C",
"hgvs_p": "p.Phe283Leu",
"transcript": "ENST00000938506.1",
"protein_id": "ENSP00000608565.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 391,
"cds_start": 847,
"cds_end": null,
"cds_length": 1176,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938506.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.844T>C",
"hgvs_p": "p.Phe282Leu",
"transcript": "NM_001010989.3",
"protein_id": "NP_001010989.1",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 390,
"cds_start": 844,
"cds_end": null,
"cds_length": 1173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001010989.3"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.844T>C",
"hgvs_p": "p.Phe282Leu",
"transcript": "ENST00000951120.1",
"protein_id": "ENSP00000621179.1",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 390,
"cds_start": 844,
"cds_end": null,
"cds_length": 1173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951120.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.847T>C",
"hgvs_p": "p.Phe283Leu",
"transcript": "ENST00000951121.1",
"protein_id": "ENSP00000621180.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 389,
"cds_start": 847,
"cds_end": null,
"cds_length": 1170,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951121.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.847T>C",
"hgvs_p": "p.Phe283Leu",
"transcript": "NM_001436349.1",
"protein_id": "NP_001423278.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 379,
"cds_start": 847,
"cds_end": null,
"cds_length": 1140,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001436349.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.772T>C",
"hgvs_p": "p.Phe258Leu",
"transcript": "NM_001436350.1",
"protein_id": "NP_001423279.1",
"transcript_support_level": null,
"aa_start": 258,
"aa_end": null,
"aa_length": 366,
"cds_start": 772,
"cds_end": null,
"cds_length": 1101,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001436350.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.772T>C",
"hgvs_p": "p.Phe258Leu",
"transcript": "ENST00000379792.6",
"protein_id": "ENSP00000369118.2",
"transcript_support_level": 5,
"aa_start": 258,
"aa_end": null,
"aa_length": 366,
"cds_start": 772,
"cds_end": null,
"cds_length": 1101,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379792.6"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.724T>C",
"hgvs_p": "p.Phe242Leu",
"transcript": "ENST00000855547.1",
"protein_id": "ENSP00000525606.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 350,
"cds_start": 724,
"cds_end": null,
"cds_length": 1053,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855547.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.721T>C",
"hgvs_p": "p.Phe241Leu",
"transcript": "NM_001436351.1",
"protein_id": "NP_001423280.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 349,
"cds_start": 721,
"cds_end": null,
"cds_length": 1050,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001436351.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.649T>C",
"hgvs_p": "p.Phe217Leu",
"transcript": "NM_001436352.1",
"protein_id": "NP_001423281.1",
"transcript_support_level": null,
"aa_start": 217,
"aa_end": null,
"aa_length": 325,
"cds_start": 649,
"cds_end": null,
"cds_length": 978,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001436352.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.568T>C",
"hgvs_p": "p.Phe190Leu",
"transcript": "NM_001436353.1",
"protein_id": "NP_001423282.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 298,
"cds_start": 568,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001436353.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.568T>C",
"hgvs_p": "p.Phe190Leu",
"transcript": "NM_001436354.1",
"protein_id": "NP_001423283.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 298,
"cds_start": 568,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001436354.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.565T>C",
"hgvs_p": "p.Phe189Leu",
"transcript": "NM_001436355.1",
"protein_id": "NP_001423284.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 297,
"cds_start": 565,
"cds_end": null,
"cds_length": 894,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001436355.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.553T>C",
"hgvs_p": "p.Phe185Leu",
"transcript": "NM_001436356.1",
"protein_id": "NP_001423285.1",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 293,
"cds_start": 553,
"cds_end": null,
"cds_length": 882,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001436356.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HERPUD1",
"gene_hgnc_id": 13744,
"hgvs_c": "c.385T>C",
"hgvs_p": "p.Phe129Leu",
"transcript": "ENST00000563911.5",
"protein_id": "ENSP00000455841.1",
"transcript_support_level": 3,
"aa_start": 129,
"aa_end": null,
"aa_length": 225,
"cds_start": 385,
"cds_end": null,
"cds_length": 678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
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],
"gene_symbol": "HERPUD1",
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"dbsnp": "rs371849429",
"frequency_reference_population": 6.840507e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
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"gnomad_exomes_ac": 1,
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"gnomad_exomes_homalt": 0,
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"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8810305595397949,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.656,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9941,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.14,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.822,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_014685.4",
"gene_symbol": "HERPUD1",
"hgnc_id": 13744,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.847T>C",
"hgvs_p": "p.Phe283Leu"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000565861.1",
"gene_symbol": "HERPUD1-IT1",
"hgnc_id": null,
"effects": [
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],
"inheritance_mode": "",
"hgvs_c": "n.-91T>C",
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}
],
"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
}