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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: 22-39521950-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=39521950&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 39521950,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001675.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "NM_182810.3",
"protein_id": "NP_877962.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 686,
"cdna_end": null,
"cdna_length": 1419,
"mane_select": "ENST00000674920.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_182810.3"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "ENST00000674920.3",
"protein_id": "ENSP00000501863.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 686,
"cdna_end": null,
"cdna_length": 1419,
"mane_select": "NM_182810.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000674920.3"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "ENST00000337304.2",
"protein_id": "ENSP00000336790.2",
"transcript_support_level": 1,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 1286,
"cdna_end": null,
"cdna_length": 2019,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000337304.2"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "ENST00000396680.3",
"protein_id": "ENSP00000379912.1",
"transcript_support_level": 1,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 768,
"cdna_end": null,
"cdna_length": 1486,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000396680.3"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "NM_001675.4",
"protein_id": "NP_001666.2",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 1291,
"cdna_end": null,
"cdna_length": 2027,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001675.4"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "ENST00000404241.7",
"protein_id": "ENSP00000384587.2",
"transcript_support_level": 5,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 1177,
"cdna_end": null,
"cdna_length": 1913,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000404241.7"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "ENST00000674568.2",
"protein_id": "ENSP00000501783.2",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 591,
"cdna_end": null,
"cdna_length": 1243,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000674568.2"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "ENST00000674835.2",
"protein_id": "ENSP00000502610.2",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 623,
"cdna_end": null,
"cdna_length": 1275,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000674835.2"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "ENST00000676346.2",
"protein_id": "ENSP00000502400.2",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 654,
"cdna_end": null,
"cdna_length": 1306,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676346.2"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "ENST00000679776.1",
"protein_id": "ENSP00000505360.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 586,
"cdna_end": null,
"cdna_length": 1238,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000679776.1"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "ENST00000921524.1",
"protein_id": "ENSP00000591583.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 892,
"cdna_end": null,
"cdna_length": 1632,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921524.1"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "ENST00000921525.1",
"protein_id": "ENSP00000591584.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 595,
"cdna_end": null,
"cdna_length": 1325,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921525.1"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "ENST00000921526.1",
"protein_id": "ENSP00000591585.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 918,
"cdna_end": null,
"cdna_length": 1654,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921526.1"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "ENST00000921527.1",
"protein_id": "ENSP00000591586.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 948,
"cdna_end": null,
"cdna_length": 1684,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921527.1"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "ENST00000921528.1",
"protein_id": "ENSP00000591587.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 621,
"cdna_end": null,
"cdna_length": 1354,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921528.1"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "ENST00000921529.1",
"protein_id": "ENSP00000591588.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 691,
"cdna_end": null,
"cdna_length": 1431,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921529.1"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "ENST00000960424.1",
"protein_id": "ENSP00000630483.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 902,
"cdna_end": null,
"cdna_length": 1631,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960424.1"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "ENST00000960425.1",
"protein_id": "ENSP00000630484.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 686,
"cdna_end": null,
"cdna_length": 1416,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960425.1"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His",
"transcript": "ENST00000960426.1",
"protein_id": "ENSP00000630485.1",
"transcript_support_level": null,
"aa_start": 135,
"aa_end": null,
"aa_length": 351,
"cds_start": 404,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 688,
"cdna_end": null,
"cdna_length": 1423,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960426.1"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.317C>A",
"hgvs_p": "p.Pro106His",
"transcript": "ENST00000675582.2",
"protein_id": "ENSP00000502056.2",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 322,
"cds_start": 317,
"cds_end": null,
"cds_length": 969,
"cdna_start": 597,
"cdna_end": null,
"cdna_length": 1249,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675582.2"
},
{
"aa_ref": "P",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.152C>A",
"hgvs_p": "p.Pro51His",
"transcript": "ENST00000680446.1",
"protein_id": "ENSP00000506657.1",
"transcript_support_level": null,
"aa_start": 51,
"aa_end": null,
"aa_length": 267,
"cds_start": 152,
"cds_end": null,
"cds_length": 804,
"cdna_start": 352,
"cdna_end": null,
"cdna_length": 1004,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000680446.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"hgvs_c": "c.*211C>A",
"hgvs_p": null,
"transcript": "ENST00000680748.1",
"protein_id": "ENSP00000506141.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 97,
"cds_start": null,
"cds_end": null,
"cds_length": 294,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 763,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000680748.1"
}
],
"gene_symbol": "ATF4",
"gene_hgnc_id": 786,
"dbsnp": "rs140428747",
"frequency_reference_population": 0.000019836769,
"hom_count_reference_population": 0,
"allele_count_reference_population": 32,
"gnomad_exomes_af": 0.0000205249,
"gnomad_genomes_af": 0.0000131992,
"gnomad_exomes_ac": 30,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4253958463668823,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.102,
"revel_prediction": "Benign",
"alphamissense_score": 0.099,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.808,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001675.4",
"gene_symbol": "ATF4",
"hgnc_id": 786,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.404C>A",
"hgvs_p": "p.Pro135His"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}