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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: 7-77571160-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=77571160&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 77571160,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000248594.11",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.182A>G",
"hgvs_p": "p.Lys61Arg",
"transcript": "NM_002835.4",
"protein_id": "NP_002826.3",
"transcript_support_level": null,
"aa_start": 61,
"aa_end": null,
"aa_length": 780,
"cds_start": 182,
"cds_end": null,
"cds_length": 2343,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 3384,
"mane_select": "ENST00000248594.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.182A>G",
"hgvs_p": "p.Lys61Arg",
"transcript": "ENST00000248594.11",
"protein_id": "ENSP00000248594.6",
"transcript_support_level": 1,
"aa_start": 61,
"aa_end": null,
"aa_length": 780,
"cds_start": 182,
"cds_end": null,
"cds_length": 2343,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 3384,
"mane_select": "NM_002835.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.-99A>G",
"hgvs_p": null,
"transcript": "ENST00000440186.5",
"protein_id": "ENSP00000413449.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 16,
"cds_start": -4,
"cds_end": null,
"cds_length": 53,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.68A>G",
"hgvs_p": "p.Lys23Arg",
"transcript": "ENST00000522115.6",
"protein_id": "ENSP00000430726.2",
"transcript_support_level": 5,
"aa_start": 23,
"aa_end": null,
"aa_length": 212,
"cds_start": 68,
"cds_end": null,
"cds_length": 640,
"cdna_start": 70,
"cdna_end": null,
"cdna_length": 642,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.263A>G",
"hgvs_p": "p.Lys88Arg",
"transcript": "XM_047420673.1",
"protein_id": "XP_047276629.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 807,
"cds_start": 263,
"cds_end": null,
"cds_length": 2424,
"cdna_start": 5100,
"cdna_end": null,
"cdna_length": 8050,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.263A>G",
"hgvs_p": "p.Lys88Arg",
"transcript": "XM_047420674.1",
"protein_id": "XP_047276630.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 775,
"cds_start": 263,
"cds_end": null,
"cds_length": 2328,
"cdna_start": 5100,
"cdna_end": null,
"cdna_length": 7954,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.182A>G",
"hgvs_p": "p.Lys61Arg",
"transcript": "XM_006716073.5",
"protein_id": "XP_006716136.1",
"transcript_support_level": null,
"aa_start": 61,
"aa_end": null,
"aa_length": 748,
"cds_start": 182,
"cds_end": null,
"cds_length": 2247,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 3288,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Arg4Gly",
"transcript": "XM_017012474.3",
"protein_id": "XP_016867963.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 665,
"cds_start": 10,
"cds_end": null,
"cds_length": 1998,
"cdna_start": 147,
"cdna_end": null,
"cdna_length": 2924,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Arg4Gly",
"transcript": "XM_047420675.1",
"protein_id": "XP_047276631.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 665,
"cds_start": 10,
"cds_end": null,
"cds_length": 1998,
"cdna_start": 677,
"cdna_end": null,
"cdna_length": 3454,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "n.212A>G",
"hgvs_p": null,
"transcript": "ENST00000460731.5",
"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": 582,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "n.*304A>G",
"hgvs_p": null,
"transcript": "ENST00000523952.5",
"protein_id": "ENSP00000428735.1",
"transcript_support_level": 4,
"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": 500,
"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": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "n.5100A>G",
"hgvs_p": null,
"transcript": "XR_007060120.1",
"protein_id": null,
"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,
"cdna_length": 7178,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.-176A>G",
"hgvs_p": null,
"transcript": "NM_001131008.2",
"protein_id": "NP_001124480.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 661,
"cds_start": -4,
"cds_end": null,
"cds_length": 1986,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3097,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.-176A>G",
"hgvs_p": null,
"transcript": "ENST00000415482.6",
"protein_id": "ENSP00000392429.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 661,
"cds_start": -4,
"cds_end": null,
"cds_length": 1986,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2316,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.-113A>G",
"hgvs_p": null,
"transcript": "NM_001131009.2",
"protein_id": "NP_001124481.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 650,
"cds_start": -4,
"cds_end": null,
"cds_length": 1953,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3001,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.-113A>G",
"hgvs_p": null,
"transcript": "ENST00000435495.6",
"protein_id": "ENSP00000397991.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 650,
"cds_start": -4,
"cds_end": null,
"cds_length": 1953,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2526,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.-176A>G",
"hgvs_p": null,
"transcript": "ENST00000418110.5",
"protein_id": "ENSP00000392526.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 85,
"cds_start": -4,
"cds_end": null,
"cds_length": 260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 564,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.-176A>G",
"hgvs_p": null,
"transcript": "ENST00000433369.6",
"protein_id": "ENSP00000404050.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 44,
"cds_start": -4,
"cds_end": null,
"cds_length": 135,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 552,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.-176A>G",
"hgvs_p": null,
"transcript": "XM_047420676.1",
"protein_id": "XP_047276632.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 661,
"cds_start": -4,
"cds_end": null,
"cds_length": 1986,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3093,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "n.*304A>G",
"hgvs_p": null,
"transcript": "ENST00000523952.5",
"protein_id": "ENSP00000428735.1",
"transcript_support_level": 4,
"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": 500,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"dbsnp": "rs121434623",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8466348648071289,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.788,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.3664,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.31,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.843,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000248594.11",
"gene_symbol": "PTPN12",
"hgnc_id": 9645,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.182A>G",
"hgvs_p": "p.Lys61Arg"
}
],
"clinvar_disease": "Carcinoma of colon",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Carcinoma of colon",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}