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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: 4-108027694-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=108027694&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 108027694,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000309522.8",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"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": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "c.643C>T",
"hgvs_p": "p.Pro215Ser",
"transcript": "NM_005327.7",
"protein_id": "NP_005318.6",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 314,
"cds_start": 643,
"cds_end": null,
"cds_length": 945,
"cdna_start": 687,
"cdna_end": null,
"cdna_length": 1803,
"mane_select": "ENST00000309522.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"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": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "c.643C>T",
"hgvs_p": "p.Pro215Ser",
"transcript": "ENST00000309522.8",
"protein_id": "ENSP00000312288.4",
"transcript_support_level": 1,
"aa_start": 215,
"aa_end": null,
"aa_length": 314,
"cds_start": 643,
"cds_end": null,
"cds_length": 945,
"cdna_start": 687,
"cdna_end": null,
"cdna_length": 1803,
"mane_select": "NM_005327.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "c.820C>T",
"hgvs_p": "p.Pro274Ser",
"transcript": "ENST00000505878.4",
"protein_id": "ENSP00000425952.2",
"transcript_support_level": 1,
"aa_start": 274,
"aa_end": null,
"aa_length": 390,
"cds_start": 820,
"cds_end": null,
"cds_length": 1173,
"cdna_start": 862,
"cdna_end": null,
"cdna_length": 1719,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "c.643C>T",
"hgvs_p": "p.Pro215Ser",
"transcript": "ENST00000603302.5",
"protein_id": "ENSP00000474560.1",
"transcript_support_level": 1,
"aa_start": 215,
"aa_end": null,
"aa_length": 331,
"cds_start": 643,
"cds_end": null,
"cds_length": 996,
"cdna_start": 862,
"cdna_end": null,
"cdna_length": 2032,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "c.643C>T",
"hgvs_p": "p.Pro215Ser",
"transcript": "NM_001184705.4",
"protein_id": "NP_001171634.3",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 331,
"cds_start": 643,
"cds_end": null,
"cds_length": 996,
"cdna_start": 687,
"cdna_end": null,
"cdna_length": 1854,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"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": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "c.655C>T",
"hgvs_p": "p.Pro219Ser",
"transcript": "NM_001331027.2",
"protein_id": "NP_001317956.2",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 318,
"cds_start": 655,
"cds_end": null,
"cds_length": 957,
"cdna_start": 818,
"cdna_end": null,
"cdna_length": 1934,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"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": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "c.655C>T",
"hgvs_p": "p.Pro219Ser",
"transcript": "ENST00000626637.2",
"protein_id": "ENSP00000486771.1",
"transcript_support_level": 2,
"aa_start": 219,
"aa_end": null,
"aa_length": 318,
"cds_start": 655,
"cds_end": null,
"cds_length": 957,
"cdna_start": 947,
"cdna_end": null,
"cdna_length": 1815,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "c.643C>T",
"hgvs_p": "p.Pro215Ser",
"transcript": "ENST00000403312.6",
"protein_id": "ENSP00000385638.3",
"transcript_support_level": 5,
"aa_start": 215,
"aa_end": null,
"aa_length": 317,
"cds_start": 643,
"cds_end": null,
"cds_length": 954,
"cdna_start": 680,
"cdna_end": null,
"cdna_length": 1752,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"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": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "c.499C>T",
"hgvs_p": "p.Pro167Ser",
"transcript": "ENST00000638559.1",
"protein_id": "ENSP00000490998.1",
"transcript_support_level": 5,
"aa_start": 167,
"aa_end": null,
"aa_length": 266,
"cds_start": 499,
"cds_end": null,
"cds_length": 801,
"cdna_start": 501,
"cdna_end": null,
"cdna_length": 1369,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "c.301C>T",
"hgvs_p": "p.Pro101Ser",
"transcript": "ENST00000682373.1",
"protein_id": "ENSP00000508283.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 200,
"cds_start": 301,
"cds_end": null,
"cds_length": 603,
"cdna_start": 302,
"cdna_end": null,
"cdna_length": 1317,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "c.229C>T",
"hgvs_p": "p.Pro77Ser",
"transcript": "ENST00000638621.1",
"protein_id": "ENSP00000491581.1",
"transcript_support_level": 5,
"aa_start": 77,
"aa_end": null,
"aa_length": 176,
"cds_start": 229,
"cds_end": null,
"cds_length": 531,
"cdna_start": 308,
"cdna_end": null,
"cdna_length": 741,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "n.4853C>T",
"hgvs_p": null,
"transcript": "ENST00000507260.3",
"protein_id": null,
"transcript_support_level": 2,
"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": 6258,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "n.1631C>T",
"hgvs_p": null,
"transcript": "ENST00000510728.6",
"protein_id": null,
"transcript_support_level": 3,
"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": 2948,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "n.76C>T",
"hgvs_p": null,
"transcript": "ENST00000514776.3",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": 6677,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "n.1830C>T",
"hgvs_p": null,
"transcript": "ENST00000515462.7",
"protein_id": null,
"transcript_support_level": 2,
"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": 3325,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "n.655C>T",
"hgvs_p": null,
"transcript": "ENST00000638648.2",
"protein_id": "ENSP00000507949.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 1976,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "n.643C>T",
"hgvs_p": null,
"transcript": "ENST00000639146.1",
"protein_id": "ENSP00000492345.1",
"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": 1964,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "n.*78C>T",
"hgvs_p": null,
"transcript": "ENST00000639335.1",
"protein_id": "ENSP00000491310.1",
"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": 1327,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "n.*117C>T",
"hgvs_p": null,
"transcript": "ENST00000640048.1",
"protein_id": "ENSP00000492009.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": 1670,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "n.*738C>T",
"hgvs_p": null,
"transcript": "ENST00000640060.1",
"protein_id": "ENSP00000492734.1",
"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": 1895,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "n.729C>T",
"hgvs_p": null,
"transcript": "ENST00000640201.2",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "n.4853C>T",
"hgvs_p": null,
"transcript": "ENST00000640752.2",
"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": 5955,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADH",
"gene_hgnc_id": 4799,
"hgvs_c": "n.*78C>T",
"hgvs_p": null,
"transcript": "ENST00000682067.1",
"protein_id": "ENSP00000507544.1",
"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,
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}
],
"gene_symbol": "HADH",
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"dbsnp": "rs140413151",
"frequency_reference_population": 0.000003742403,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000275644,
"gnomad_genomes_af": 0.0000131491,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9360342025756836,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.888,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.4927,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.43,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.168,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.05,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
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"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000309522.8",
"gene_symbol": "HADH",
"hgnc_id": 4799,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.643C>T",
"hgvs_p": "p.Pro215Ser"
}
],
"clinvar_disease": "Deficiency of 3-hydroxyacyl-CoA dehydrogenase,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Deficiency of 3-hydroxyacyl-CoA dehydrogenase|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}