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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: 7-100105984-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=100105984&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 100105984,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001363671.2",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.955T>C",
"hgvs_p": "p.Cys319Arg",
"transcript": "NM_004722.4",
"protein_id": "NP_004713.2",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 453,
"cds_start": 955,
"cds_end": null,
"cds_length": 1362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000359593.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004722.4"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.955T>C",
"hgvs_p": "p.Cys319Arg",
"transcript": "ENST00000359593.9",
"protein_id": "ENSP00000352603.4",
"transcript_support_level": 1,
"aa_start": 319,
"aa_end": null,
"aa_length": 453,
"cds_start": 955,
"cds_end": null,
"cds_length": 1362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004722.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000359593.9"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.955T>C",
"hgvs_p": "p.Cys319Arg",
"transcript": "ENST00000421755.5",
"protein_id": "ENSP00000412185.1",
"transcript_support_level": 1,
"aa_start": 319,
"aa_end": null,
"aa_length": 453,
"cds_start": 955,
"cds_end": null,
"cds_length": 1362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000421755.5"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.976T>C",
"hgvs_p": "p.Cys326Arg",
"transcript": "NM_001363671.2",
"protein_id": "NP_001350600.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 460,
"cds_start": 976,
"cds_end": null,
"cds_length": 1383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001363671.2"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.976T>C",
"hgvs_p": "p.Cys326Arg",
"transcript": "NM_001438824.1",
"protein_id": "NP_001425753.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 460,
"cds_start": 976,
"cds_end": null,
"cds_length": 1383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001438824.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.976T>C",
"hgvs_p": "p.Cys326Arg",
"transcript": "ENST00000429084.5",
"protein_id": "ENSP00000403663.1",
"transcript_support_level": 5,
"aa_start": 326,
"aa_end": null,
"aa_length": 460,
"cds_start": 976,
"cds_end": null,
"cds_length": 1383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000429084.5"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.976T>C",
"hgvs_p": "p.Cys326Arg",
"transcript": "ENST00000907395.1",
"protein_id": "ENSP00000577454.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 460,
"cds_start": 976,
"cds_end": null,
"cds_length": 1383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000907395.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.976T>C",
"hgvs_p": "p.Cys326Arg",
"transcript": "ENST00000918985.1",
"protein_id": "ENSP00000589044.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 460,
"cds_start": 976,
"cds_end": null,
"cds_length": 1383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918985.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.970T>C",
"hgvs_p": "p.Cys324Arg",
"transcript": "ENST00000970615.1",
"protein_id": "ENSP00000640674.1",
"transcript_support_level": null,
"aa_start": 324,
"aa_end": null,
"aa_length": 458,
"cds_start": 970,
"cds_end": null,
"cds_length": 1377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970615.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.961T>C",
"hgvs_p": "p.Cys321Arg",
"transcript": "ENST00000970616.1",
"protein_id": "ENSP00000640675.1",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 455,
"cds_start": 961,
"cds_end": null,
"cds_length": 1368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970616.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.955T>C",
"hgvs_p": "p.Cys319Arg",
"transcript": "NM_001438825.1",
"protein_id": "NP_001425754.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 453,
"cds_start": 955,
"cds_end": null,
"cds_length": 1362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001438825.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.955T>C",
"hgvs_p": "p.Cys319Arg",
"transcript": "NM_001438826.1",
"protein_id": "NP_001425755.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 453,
"cds_start": 955,
"cds_end": null,
"cds_length": 1362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001438826.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.955T>C",
"hgvs_p": "p.Cys319Arg",
"transcript": "ENST00000713591.1",
"protein_id": "ENSP00000518888.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 453,
"cds_start": 955,
"cds_end": null,
"cds_length": 1362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000713591.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.955T>C",
"hgvs_p": "p.Cys319Arg",
"transcript": "ENST00000713791.1",
"protein_id": "ENSP00000519097.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 453,
"cds_start": 955,
"cds_end": null,
"cds_length": 1362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000713791.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.946T>C",
"hgvs_p": "p.Cys316Arg",
"transcript": "ENST00000713792.1",
"protein_id": "ENSP00000519098.1",
"transcript_support_level": null,
"aa_start": 316,
"aa_end": null,
"aa_length": 450,
"cds_start": 946,
"cds_end": null,
"cds_length": 1353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000713792.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.940T>C",
"hgvs_p": "p.Cys314Arg",
"transcript": "ENST00000970614.1",
"protein_id": "ENSP00000640673.1",
"transcript_support_level": null,
"aa_start": 314,
"aa_end": null,
"aa_length": 448,
"cds_start": 940,
"cds_end": null,
"cds_length": 1347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970614.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.976T>C",
"hgvs_p": "p.Cys326Arg",
"transcript": "ENST00000970617.1",
"protein_id": "ENSP00000640676.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 443,
"cds_start": 976,
"cds_end": null,
"cds_length": 1332,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970617.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.955T>C",
"hgvs_p": "p.Cys319Arg",
"transcript": "ENST00000907397.1",
"protein_id": "ENSP00000577456.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 436,
"cds_start": 955,
"cds_end": null,
"cds_length": 1311,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000907397.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.901T>C",
"hgvs_p": "p.Cys301Arg",
"transcript": "ENST00000970618.1",
"protein_id": "ENSP00000640677.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 435,
"cds_start": 901,
"cds_end": null,
"cds_length": 1308,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970618.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.976T>C",
"hgvs_p": "p.Cys326Arg",
"transcript": "NM_001438827.1",
"protein_id": "NP_001425756.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 419,
"cds_start": 976,
"cds_end": null,
"cds_length": 1260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001438827.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.976T>C",
"hgvs_p": "p.Cys326Arg",
"transcript": "ENST00000918987.1",
"protein_id": "ENSP00000589046.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 419,
"cds_start": 976,
"cds_end": null,
"cds_length": 1260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918987.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4M1",
"gene_hgnc_id": 574,
"hgvs_c": "c.955T>C",
"hgvs_p": "p.Cys319Arg",
"transcript": "NM_001438828.1",
"protein_id": "NP_001425757.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 412,
"cds_start": 955,
"cds_end": null,
"cds_length": 1239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
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],
"gene_symbol": "AP4M1",
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"dbsnp": "rs754498075",
"frequency_reference_population": 0.000009293519,
"hom_count_reference_population": 0,
"allele_count_reference_population": 15,
"gnomad_exomes_af": 0.00000957676,
"gnomad_genomes_af": 0.0000065722,
"gnomad_exomes_ac": 14,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8491066098213196,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.483,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9937,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.162,
"phylop100way_prediction": "Uncertain_significance",
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PM5",
"PP3_Moderate",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001363671.2",
"gene_symbol": "AP4M1",
"hgnc_id": 574,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.976T>C",
"hgvs_p": "p.Cys326Arg"
}
],
"clinvar_disease": "Hereditary spastic paraplegia 50,Inborn genetic diseases,Spastic paraplegia,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 LP:2 US:1",
"phenotype_combined": "not specified|Spastic paraplegia|Hereditary spastic paraplegia 50|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}