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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: 7-77626750-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=77626750&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 77626750,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_002835.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.1071G>A",
"hgvs_p": "p.Pro357Pro",
"transcript": "NM_002835.4",
"protein_id": "NP_002826.3",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 780,
"cds_start": 1071,
"cds_end": null,
"cds_length": 2343,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000248594.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002835.4"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.1071G>A",
"hgvs_p": "p.Pro357Pro",
"transcript": "ENST00000248594.11",
"protein_id": "ENSP00000248594.6",
"transcript_support_level": 1,
"aa_start": 357,
"aa_end": null,
"aa_length": 780,
"cds_start": 1071,
"cds_end": null,
"cds_length": 2343,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002835.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000248594.11"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.1068G>A",
"hgvs_p": "p.Pro356Pro",
"transcript": "ENST00000962769.1",
"protein_id": "ENSP00000632828.1",
"transcript_support_level": null,
"aa_start": 356,
"aa_end": null,
"aa_length": 779,
"cds_start": 1068,
"cds_end": null,
"cds_length": 2340,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962769.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.900G>A",
"hgvs_p": "p.Pro300Pro",
"transcript": "ENST00000962770.1",
"protein_id": "ENSP00000632829.1",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 723,
"cds_start": 900,
"cds_end": null,
"cds_length": 2172,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962770.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.894G>A",
"hgvs_p": "p.Pro298Pro",
"transcript": "ENST00000928330.1",
"protein_id": "ENSP00000598389.1",
"transcript_support_level": null,
"aa_start": 298,
"aa_end": null,
"aa_length": 721,
"cds_start": 894,
"cds_end": null,
"cds_length": 2166,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000928330.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.714G>A",
"hgvs_p": "p.Pro238Pro",
"transcript": "NM_001131008.2",
"protein_id": "NP_001124480.1",
"transcript_support_level": null,
"aa_start": 238,
"aa_end": null,
"aa_length": 661,
"cds_start": 714,
"cds_end": null,
"cds_length": 1986,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001131008.2"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.714G>A",
"hgvs_p": "p.Pro238Pro",
"transcript": "ENST00000415482.6",
"protein_id": "ENSP00000392429.2",
"transcript_support_level": 5,
"aa_start": 238,
"aa_end": null,
"aa_length": 661,
"cds_start": 714,
"cds_end": null,
"cds_length": 1986,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000415482.6"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.681G>A",
"hgvs_p": "p.Pro227Pro",
"transcript": "NM_001131009.2",
"protein_id": "NP_001124481.1",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 650,
"cds_start": 681,
"cds_end": null,
"cds_length": 1953,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001131009.2"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.681G>A",
"hgvs_p": "p.Pro227Pro",
"transcript": "ENST00000435495.6",
"protein_id": "ENSP00000397991.2",
"transcript_support_level": 2,
"aa_start": 227,
"aa_end": null,
"aa_length": 650,
"cds_start": 681,
"cds_end": null,
"cds_length": 1953,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000435495.6"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.1152G>A",
"hgvs_p": "p.Pro384Pro",
"transcript": "XM_047420673.1",
"protein_id": "XP_047276629.1",
"transcript_support_level": null,
"aa_start": 384,
"aa_end": null,
"aa_length": 807,
"cds_start": 1152,
"cds_end": null,
"cds_length": 2424,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420673.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.1056G>A",
"hgvs_p": "p.Pro352Pro",
"transcript": "XM_047420674.1",
"protein_id": "XP_047276630.1",
"transcript_support_level": null,
"aa_start": 352,
"aa_end": null,
"aa_length": 775,
"cds_start": 1056,
"cds_end": null,
"cds_length": 2328,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420674.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.975G>A",
"hgvs_p": "p.Pro325Pro",
"transcript": "XM_006716073.5",
"protein_id": "XP_006716136.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 748,
"cds_start": 975,
"cds_end": null,
"cds_length": 2247,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006716073.5"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.726G>A",
"hgvs_p": "p.Pro242Pro",
"transcript": "XM_017012474.3",
"protein_id": "XP_016867963.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 665,
"cds_start": 726,
"cds_end": null,
"cds_length": 1998,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017012474.3"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.726G>A",
"hgvs_p": "p.Pro242Pro",
"transcript": "XM_047420675.1",
"protein_id": "XP_047276631.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 665,
"cds_start": 726,
"cds_end": null,
"cds_length": 1998,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420675.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.714G>A",
"hgvs_p": "p.Pro238Pro",
"transcript": "XM_047420676.1",
"protein_id": "XP_047276632.1",
"transcript_support_level": null,
"aa_start": 238,
"aa_end": null,
"aa_length": 661,
"cds_start": 714,
"cds_end": null,
"cds_length": 1986,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420676.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.432G>A",
"hgvs_p": "p.Pro144Pro",
"transcript": "XM_047420677.1",
"protein_id": "XP_047276633.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 567,
"cds_start": 432,
"cds_end": null,
"cds_length": 1704,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420677.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "n.5989G>A",
"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": 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": "XR_007060120.1"
}
],
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"dbsnp": "rs754211441",
"frequency_reference_population": 0.000015513438,
"hom_count_reference_population": 0,
"allele_count_reference_population": 25,
"gnomad_exomes_af": 0.0000164462,
"gnomad_genomes_af": 0.00000657013,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7200000286102295,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.72,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.804,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BP7,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_002835.4",
"gene_symbol": "PTPN12",
"hgnc_id": 9645,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1071G>A",
"hgvs_p": "p.Pro357Pro"
}
],
"clinvar_disease": "PTPN12-related disorder",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "PTPN12-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}