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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: 11-71165389-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=71165389&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 71165389,
"ref": "T",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000601538.6",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "NM_012309.5",
"protein_id": "NP_036441.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1849,
"cds_start": -4,
"cds_end": null,
"cds_length": 5550,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10830,
"mane_select": "ENST00000601538.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "ENST00000601538.6",
"protein_id": "ENSP00000469689.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1849,
"cds_start": -4,
"cds_end": null,
"cds_length": 5550,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10830,
"mane_select": "NM_012309.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "NM_001441024.1",
"protein_id": "NP_001427953.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1889,
"cds_start": -4,
"cds_end": null,
"cds_length": 5670,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10950,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "NM_001441025.1",
"protein_id": "NP_001427954.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1832,
"cds_start": -4,
"cds_end": null,
"cds_length": 5499,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10779,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "NM_001441026.1",
"protein_id": "NP_001427955.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1832,
"cds_start": -4,
"cds_end": null,
"cds_length": 5499,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10906,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "NM_001441027.1",
"protein_id": "NP_001427956.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1832,
"cds_start": -4,
"cds_end": null,
"cds_length": 5499,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11039,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "NM_001441028.1",
"protein_id": "NP_001427957.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1832,
"cds_start": -4,
"cds_end": null,
"cds_length": 5499,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "NM_001441029.1",
"protein_id": "NP_001427958.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1832,
"cds_start": -4,
"cds_end": null,
"cds_length": 5499,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10912,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "NM_001441030.1",
"protein_id": "NP_001427959.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1832,
"cds_start": -4,
"cds_end": null,
"cds_length": 5499,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10826,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "NM_001441031.1",
"protein_id": "NP_001427960.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1832,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 11085,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "NM_001441032.1",
"protein_id": "NP_001427961.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1832,
"cds_start": -4,
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"cdna_length": 10710,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 3,
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"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "NM_001441033.1",
"protein_id": "NP_001427962.1",
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"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 11036,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "NM_001441034.1",
"protein_id": "NP_001427963.1",
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 23,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "NM_001441035.1",
"protein_id": "NP_001427964.1",
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"aa_start": null,
"aa_end": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 24,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "NM_001441036.1",
"protein_id": "NP_001427965.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "NM_001441037.1",
"protein_id": "NP_001427966.1",
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},
{
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"intron_variant"
],
"exon_rank": null,
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"exon_count": 22,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "NM_001441038.1",
"protein_id": "NP_001427967.1",
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "NM_001441039.1",
"protein_id": "NP_001427968.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 1657,
"cds_start": -4,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "XM_017017388.2",
"protein_id": "XP_016872877.1",
"transcript_support_level": null,
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"cdna_length": 11136,
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 26,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null,
"transcript": "XM_017017389.2",
"protein_id": "XP_016872878.1",
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}
],
"gene_symbol": "SHANK2",
"gene_hgnc_id": 14295,
"dbsnp": "rs7124728",
"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": -0.9100000262260437,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.91,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.238,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000601538.6",
"gene_symbol": "SHANK2",
"hgnc_id": 14295,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-12-18051A>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}