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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: 12-57727716-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=57727716&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 57727716,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001122772.3",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"hgvs_c": "c.2822A>T",
"hgvs_p": "p.Lys941Met",
"transcript": "NM_001122772.3",
"protein_id": "NP_001116244.1",
"transcript_support_level": null,
"aa_start": 941,
"aa_end": null,
"aa_length": 1192,
"cds_start": 2822,
"cds_end": null,
"cds_length": 3579,
"cdna_start": 3318,
"cdna_end": null,
"cdna_length": 5430,
"mane_select": "ENST00000547588.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"hgvs_c": "c.2822A>T",
"hgvs_p": "p.Lys941Met",
"transcript": "ENST00000547588.6",
"protein_id": "ENSP00000449241.1",
"transcript_support_level": 1,
"aa_start": 941,
"aa_end": null,
"aa_length": 1192,
"cds_start": 2822,
"cds_end": null,
"cds_length": 3579,
"cdna_start": 3318,
"cdna_end": null,
"cdna_length": 5430,
"mane_select": "NM_001122772.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"hgvs_c": "c.1754A>T",
"hgvs_p": "p.Lys585Met",
"transcript": "ENST00000257897.7",
"protein_id": "ENSP00000257897.3",
"transcript_support_level": 1,
"aa_start": 585,
"aa_end": null,
"aa_length": 836,
"cds_start": 1754,
"cds_end": null,
"cds_length": 2511,
"cdna_start": 1840,
"cdna_end": null,
"cdna_length": 5388,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2-AS1",
"gene_hgnc_id": 48633,
"hgvs_c": "n.860T>A",
"hgvs_p": null,
"transcript": "ENST00000542466.2",
"protein_id": null,
"transcript_support_level": 1,
"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": 1500,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"hgvs_c": "c.2351A>T",
"hgvs_p": "p.Lys784Met",
"transcript": "ENST00000328568.9",
"protein_id": "ENSP00000328160.4",
"transcript_support_level": 5,
"aa_start": 784,
"aa_end": null,
"aa_length": 1035,
"cds_start": 2351,
"cds_end": null,
"cds_length": 3108,
"cdna_start": 2352,
"cdna_end": null,
"cdna_length": 4464,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"hgvs_c": "c.1754A>T",
"hgvs_p": "p.Lys585Met",
"transcript": "NM_014770.4",
"protein_id": "NP_055585.1",
"transcript_support_level": null,
"aa_start": 585,
"aa_end": null,
"aa_length": 836,
"cds_start": 1754,
"cds_end": null,
"cds_length": 2511,
"cdna_start": 1844,
"cdna_end": null,
"cdna_length": 5392,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"hgvs_c": "c.2762A>T",
"hgvs_p": "p.Lys921Met",
"transcript": "XM_005268625.4",
"protein_id": "XP_005268682.1",
"transcript_support_level": null,
"aa_start": 921,
"aa_end": null,
"aa_length": 1172,
"cds_start": 2762,
"cds_end": null,
"cds_length": 3519,
"cdna_start": 3258,
"cdna_end": null,
"cdna_length": 6806,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"hgvs_c": "c.1814A>T",
"hgvs_p": "p.Lys605Met",
"transcript": "XM_005268626.3",
"protein_id": "XP_005268683.1",
"transcript_support_level": null,
"aa_start": 605,
"aa_end": null,
"aa_length": 856,
"cds_start": 1814,
"cds_end": null,
"cds_length": 2571,
"cdna_start": 1904,
"cdna_end": null,
"cdna_length": 5452,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP2-AS1",
"gene_hgnc_id": 48633,
"hgvs_c": "n.891T>A",
"hgvs_p": null,
"transcript": "NR_027032.1",
"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": 1531,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OS9",
"gene_hgnc_id": 16994,
"hgvs_c": "c.*723T>A",
"hgvs_p": null,
"transcript": "ENST00000700670.1",
"protein_id": "ENSP00000515138.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 104,
"cds_start": -4,
"cds_end": null,
"cds_length": 315,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1666,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AGAP2",
"gene_hgnc_id": 16921,
"dbsnp": "rs1347314682",
"frequency_reference_population": 6.8862556e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.88626e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.48866283893585205,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.349,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.278,
"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": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001122772.3",
"gene_symbol": "AGAP2",
"hgnc_id": 16921,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2822A>T",
"hgvs_p": "p.Lys941Met"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000542466.2",
"gene_symbol": "AGAP2-AS1",
"hgnc_id": 48633,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.860T>A",
"hgvs_p": null
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000700670.1",
"gene_symbol": "OS9",
"hgnc_id": 16994,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*723T>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}