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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: 7-77618504-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=77618504&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 77618504,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000248594.11",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.964G>A",
"hgvs_p": "p.Val322Ile",
"transcript": "NM_002835.4",
"protein_id": "NP_002826.3",
"transcript_support_level": null,
"aa_start": 322,
"aa_end": null,
"aa_length": 780,
"cds_start": 964,
"cds_end": null,
"cds_length": 2343,
"cdna_start": 1216,
"cdna_end": null,
"cdna_length": 3384,
"mane_select": "ENST00000248594.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.964G>A",
"hgvs_p": "p.Val322Ile",
"transcript": "ENST00000248594.11",
"protein_id": "ENSP00000248594.6",
"transcript_support_level": 1,
"aa_start": 322,
"aa_end": null,
"aa_length": 780,
"cds_start": 964,
"cds_end": null,
"cds_length": 2343,
"cdna_start": 1216,
"cdna_end": null,
"cdna_length": 3384,
"mane_select": "NM_002835.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.607G>A",
"hgvs_p": "p.Val203Ile",
"transcript": "NM_001131008.2",
"protein_id": "NP_001124480.1",
"transcript_support_level": null,
"aa_start": 203,
"aa_end": null,
"aa_length": 661,
"cds_start": 607,
"cds_end": null,
"cds_length": 1986,
"cdna_start": 929,
"cdna_end": null,
"cdna_length": 3097,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.607G>A",
"hgvs_p": "p.Val203Ile",
"transcript": "ENST00000415482.6",
"protein_id": "ENSP00000392429.2",
"transcript_support_level": 5,
"aa_start": 203,
"aa_end": null,
"aa_length": 661,
"cds_start": 607,
"cds_end": null,
"cds_length": 1986,
"cdna_start": 937,
"cdna_end": null,
"cdna_length": 2316,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.574G>A",
"hgvs_p": "p.Val192Ile",
"transcript": "NM_001131009.2",
"protein_id": "NP_001124481.1",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 650,
"cds_start": 574,
"cds_end": null,
"cds_length": 1953,
"cdna_start": 833,
"cdna_end": null,
"cdna_length": 3001,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.574G>A",
"hgvs_p": "p.Val192Ile",
"transcript": "ENST00000435495.6",
"protein_id": "ENSP00000397991.2",
"transcript_support_level": 2,
"aa_start": 192,
"aa_end": null,
"aa_length": 650,
"cds_start": 574,
"cds_end": null,
"cds_length": 1953,
"cdna_start": 807,
"cdna_end": null,
"cdna_length": 2526,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.1045G>A",
"hgvs_p": "p.Val349Ile",
"transcript": "XM_047420673.1",
"protein_id": "XP_047276629.1",
"transcript_support_level": null,
"aa_start": 349,
"aa_end": null,
"aa_length": 807,
"cds_start": 1045,
"cds_end": null,
"cds_length": 2424,
"cdna_start": 5882,
"cdna_end": null,
"cdna_length": 8050,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.949G>A",
"hgvs_p": "p.Val317Ile",
"transcript": "XM_047420674.1",
"protein_id": "XP_047276630.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 775,
"cds_start": 949,
"cds_end": null,
"cds_length": 2328,
"cdna_start": 5786,
"cdna_end": null,
"cdna_length": 7954,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.868G>A",
"hgvs_p": "p.Val290Ile",
"transcript": "XM_006716073.5",
"protein_id": "XP_006716136.1",
"transcript_support_level": null,
"aa_start": 290,
"aa_end": null,
"aa_length": 748,
"cds_start": 868,
"cds_end": null,
"cds_length": 2247,
"cdna_start": 1120,
"cdna_end": null,
"cdna_length": 3288,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.619G>A",
"hgvs_p": "p.Val207Ile",
"transcript": "XM_017012474.3",
"protein_id": "XP_016867963.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 665,
"cds_start": 619,
"cds_end": null,
"cds_length": 1998,
"cdna_start": 756,
"cdna_end": null,
"cdna_length": 2924,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.619G>A",
"hgvs_p": "p.Val207Ile",
"transcript": "XM_047420675.1",
"protein_id": "XP_047276631.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 665,
"cds_start": 619,
"cds_end": null,
"cds_length": 1998,
"cdna_start": 1286,
"cdna_end": null,
"cdna_length": 3454,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.607G>A",
"hgvs_p": "p.Val203Ile",
"transcript": "XM_047420676.1",
"protein_id": "XP_047276632.1",
"transcript_support_level": null,
"aa_start": 203,
"aa_end": null,
"aa_length": 661,
"cds_start": 607,
"cds_end": null,
"cds_length": 1986,
"cdna_start": 925,
"cdna_end": null,
"cdna_length": 3093,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "c.325G>A",
"hgvs_p": "p.Val109Ile",
"transcript": "XM_047420677.1",
"protein_id": "XP_047276633.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 567,
"cds_start": 325,
"cds_end": null,
"cds_length": 1704,
"cdna_start": 440,
"cdna_end": null,
"cdna_length": 2608,
"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": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"hgvs_c": "n.5882G>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": -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
}
],
"gene_symbol": "PTPN12",
"gene_hgnc_id": 9645,
"dbsnp": "rs9640663",
"frequency_reference_population": 0.62131405,
"hom_count_reference_population": 315015,
"allele_count_reference_population": 992579,
"gnomad_exomes_af": 0.61441,
"gnomad_genomes_af": 0.687006,
"gnomad_exomes_ac": 888205,
"gnomad_genomes_ac": 104374,
"gnomad_exomes_homalt": 278067,
"gnomad_genomes_homalt": 36948,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 6.785749064874835e-7,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.052,
"revel_prediction": "Benign",
"alphamissense_score": 0.0733,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.67,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.398,
"phylop100way_prediction": "Benign",
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000248594.11",
"gene_symbol": "PTPN12",
"hgnc_id": 9645,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.964G>A",
"hgvs_p": "p.Val322Ile"
}
],
"clinvar_disease": "PTPN12-related disorder",
"clinvar_classification": "Benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "PTPN12-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}