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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: 12-111446790-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=111446790&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 111446790,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_005475.3",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2B3",
"gene_hgnc_id": 29605,
"hgvs_c": "c.770T>C",
"hgvs_p": "p.Ile257Thr",
"transcript": "NM_005475.3",
"protein_id": "NP_005466.1",
"transcript_support_level": null,
"aa_start": 257,
"aa_end": null,
"aa_length": 575,
"cds_start": 770,
"cds_end": null,
"cds_length": 1728,
"cdna_start": 1152,
"cdna_end": null,
"cdna_length": 5431,
"mane_select": "ENST00000341259.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2B3",
"gene_hgnc_id": 29605,
"hgvs_c": "c.770T>C",
"hgvs_p": "p.Ile257Thr",
"transcript": "ENST00000341259.7",
"protein_id": "ENSP00000345492.2",
"transcript_support_level": 1,
"aa_start": 257,
"aa_end": null,
"aa_length": 575,
"cds_start": 770,
"cds_end": null,
"cds_length": 1728,
"cdna_start": 1152,
"cdna_end": null,
"cdna_length": 5431,
"mane_select": "NM_005475.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2B3",
"gene_hgnc_id": 29605,
"hgvs_c": "c.164T>C",
"hgvs_p": "p.Ile55Thr",
"transcript": "NM_001291424.1",
"protein_id": "NP_001278353.1",
"transcript_support_level": null,
"aa_start": 55,
"aa_end": null,
"aa_length": 373,
"cds_start": 164,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 204,
"cdna_end": null,
"cdna_length": 4483,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2B3",
"gene_hgnc_id": 29605,
"hgvs_c": "c.164T>C",
"hgvs_p": "p.Ile55Thr",
"transcript": "ENST00000538307.1",
"protein_id": "ENSP00000440597.1",
"transcript_support_level": 2,
"aa_start": 55,
"aa_end": null,
"aa_length": 373,
"cds_start": 164,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 204,
"cdna_end": null,
"cdna_length": 2062,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2B3",
"gene_hgnc_id": 29605,
"hgvs_c": "c.890T>C",
"hgvs_p": "p.Ile297Thr",
"transcript": "XM_011537719.3",
"protein_id": "XP_011536021.1",
"transcript_support_level": null,
"aa_start": 297,
"aa_end": null,
"aa_length": 616,
"cds_start": 890,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1272,
"cdna_end": null,
"cdna_length": 5554,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2B3",
"gene_hgnc_id": 29605,
"hgvs_c": "c.890T>C",
"hgvs_p": "p.Ile297Thr",
"transcript": "XM_011537720.4",
"protein_id": "XP_011536022.1",
"transcript_support_level": null,
"aa_start": 297,
"aa_end": null,
"aa_length": 616,
"cds_start": 890,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1312,
"cdna_end": null,
"cdna_length": 5594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2B3",
"gene_hgnc_id": 29605,
"hgvs_c": "c.890T>C",
"hgvs_p": "p.Ile297Thr",
"transcript": "XM_005253818.5",
"protein_id": "XP_005253875.1",
"transcript_support_level": null,
"aa_start": 297,
"aa_end": null,
"aa_length": 615,
"cds_start": 890,
"cds_end": null,
"cds_length": 1848,
"cdna_start": 1272,
"cdna_end": null,
"cdna_length": 5551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2B3",
"gene_hgnc_id": 29605,
"hgvs_c": "c.890T>C",
"hgvs_p": "p.Ile297Thr",
"transcript": "XM_047428025.1",
"protein_id": "XP_047283981.1",
"transcript_support_level": null,
"aa_start": 297,
"aa_end": null,
"aa_length": 615,
"cds_start": 890,
"cds_end": null,
"cds_length": 1848,
"cdna_start": 1312,
"cdna_end": null,
"cdna_length": 5591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2B3",
"gene_hgnc_id": 29605,
"hgvs_c": "c.770T>C",
"hgvs_p": "p.Ile257Thr",
"transcript": "XM_005253819.5",
"protein_id": "XP_005253876.1",
"transcript_support_level": null,
"aa_start": 257,
"aa_end": null,
"aa_length": 576,
"cds_start": 770,
"cds_end": null,
"cds_length": 1731,
"cdna_start": 1152,
"cdna_end": null,
"cdna_length": 5434,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2B3",
"gene_hgnc_id": 29605,
"hgvs_c": "c.770T>C",
"hgvs_p": "p.Ile257Thr",
"transcript": "XM_047428026.1",
"protein_id": "XP_047283982.1",
"transcript_support_level": null,
"aa_start": 257,
"aa_end": null,
"aa_length": 575,
"cds_start": 770,
"cds_end": null,
"cds_length": 1728,
"cdna_start": 1192,
"cdna_end": null,
"cdna_length": 5471,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2B3",
"gene_hgnc_id": 29605,
"hgvs_c": "c.1000T>C",
"hgvs_p": "p.Ser334Pro",
"transcript": "XM_047428027.1",
"protein_id": "XP_047283983.1",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 353,
"cds_start": 1000,
"cds_end": null,
"cds_length": 1062,
"cdna_start": 1382,
"cdna_end": null,
"cdna_length": 1539,
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2B3",
"gene_hgnc_id": 29605,
"hgvs_c": "c.-32T>C",
"hgvs_p": null,
"transcript": "XM_006719180.5",
"protein_id": "XP_006719243.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 309,
"cds_start": -4,
"cds_end": null,
"cds_length": 930,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5509,
"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": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2B3",
"gene_hgnc_id": 29605,
"hgvs_c": "c.-32T>C",
"hgvs_p": null,
"transcript": "XM_047428028.1",
"protein_id": "XP_047283984.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 308,
"cds_start": -4,
"cds_end": null,
"cds_length": 927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4538,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "ATXN2",
"gene_hgnc_id": 10555,
"hgvs_c": "n.*171-2603A>G",
"hgvs_p": null,
"transcript": "ENST00000642389.2",
"protein_id": "ENSP00000496055.2",
"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": 4438,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SH2B3",
"gene_hgnc_id": 29605,
"dbsnp": "rs147341899",
"frequency_reference_population": 0.00040165317,
"hom_count_reference_population": 5,
"allele_count_reference_population": 628,
"gnomad_exomes_af": 0.000255799,
"gnomad_genomes_af": 0.00175344,
"gnomad_exomes_ac": 361,
"gnomad_genomes_ac": 267,
"gnomad_exomes_homalt": 4,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.008188217878341675,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.325,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8816,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.369,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.03,
"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,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_005475.3",
"gene_symbol": "SH2B3",
"hgnc_id": 29605,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AR",
"hgvs_c": "c.770T>C",
"hgvs_p": "p.Ile257Thr"
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000642389.2",
"gene_symbol": "ATXN2",
"hgnc_id": 10555,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "n.*171-2603A>G",
"hgvs_p": null
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1 B:1",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}