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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: 11-10500245-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=10500245&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 10500245,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000396553.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD3",
"gene_hgnc_id": 470,
"hgvs_c": "c.1717C>T",
"hgvs_p": "p.Arg573Cys",
"transcript": "NM_001025389.2",
"protein_id": "NP_001020560.1",
"transcript_support_level": null,
"aa_start": 573,
"aa_end": null,
"aa_length": 767,
"cds_start": 1717,
"cds_end": null,
"cds_length": 2304,
"cdna_start": 1907,
"cdna_end": null,
"cdna_length": 4189,
"mane_select": "ENST00000396553.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD3",
"gene_hgnc_id": 470,
"hgvs_c": "c.1717C>T",
"hgvs_p": "p.Arg573Cys",
"transcript": "ENST00000396553.7",
"protein_id": "ENSP00000379801.2",
"transcript_support_level": 1,
"aa_start": 573,
"aa_end": null,
"aa_length": 767,
"cds_start": 1717,
"cds_end": null,
"cds_length": 2304,
"cdna_start": 1907,
"cdna_end": null,
"cdna_length": 4189,
"mane_select": "NM_001025389.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD3",
"gene_hgnc_id": 470,
"hgvs_c": "c.1744C>T",
"hgvs_p": "p.Arg582Cys",
"transcript": "ENST00000396554.7",
"protein_id": "ENSP00000379802.3",
"transcript_support_level": 1,
"aa_start": 582,
"aa_end": null,
"aa_length": 776,
"cds_start": 1744,
"cds_end": null,
"cds_length": 2331,
"cdna_start": 2085,
"cdna_end": null,
"cdna_length": 3806,
"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": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD3",
"gene_hgnc_id": 470,
"hgvs_c": "n.*1070C>T",
"hgvs_p": null,
"transcript": "ENST00000534047.5",
"protein_id": "ENSP00000433937.1",
"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": 2376,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD3",
"gene_hgnc_id": 470,
"hgvs_c": "n.*1070C>T",
"hgvs_p": null,
"transcript": "ENST00000534047.5",
"protein_id": "ENSP00000433937.1",
"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": 2376,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD3",
"gene_hgnc_id": 470,
"hgvs_c": "c.1744C>T",
"hgvs_p": "p.Arg582Cys",
"transcript": "NM_000480.3",
"protein_id": "NP_000471.1",
"transcript_support_level": null,
"aa_start": 582,
"aa_end": null,
"aa_length": 776,
"cds_start": 1744,
"cds_end": null,
"cds_length": 2331,
"cdna_start": 2075,
"cdna_end": null,
"cdna_length": 4357,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD3",
"gene_hgnc_id": 470,
"hgvs_c": "c.1738C>T",
"hgvs_p": "p.Arg580Cys",
"transcript": "NM_001025390.2",
"protein_id": "NP_001020561.1",
"transcript_support_level": null,
"aa_start": 580,
"aa_end": null,
"aa_length": 774,
"cds_start": 1738,
"cds_end": null,
"cds_length": 2325,
"cdna_start": 2069,
"cdna_end": null,
"cdna_length": 4351,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD3",
"gene_hgnc_id": 470,
"hgvs_c": "c.1738C>T",
"hgvs_p": "p.Arg580Cys",
"transcript": "ENST00000528723.5",
"protein_id": "ENSP00000436987.1",
"transcript_support_level": 2,
"aa_start": 580,
"aa_end": null,
"aa_length": 774,
"cds_start": 1738,
"cds_end": null,
"cds_length": 2325,
"cdna_start": 1939,
"cdna_end": null,
"cdna_length": 2753,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD3",
"gene_hgnc_id": 470,
"hgvs_c": "c.1717C>T",
"hgvs_p": "p.Arg573Cys",
"transcript": "NM_001172430.1",
"protein_id": "NP_001165901.1",
"transcript_support_level": null,
"aa_start": 573,
"aa_end": null,
"aa_length": 767,
"cds_start": 1717,
"cds_end": null,
"cds_length": 2304,
"cdna_start": 2016,
"cdna_end": null,
"cdna_length": 4298,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD3",
"gene_hgnc_id": 470,
"hgvs_c": "c.1717C>T",
"hgvs_p": "p.Arg573Cys",
"transcript": "ENST00000529507.5",
"protein_id": "ENSP00000431648.1",
"transcript_support_level": 2,
"aa_start": 573,
"aa_end": null,
"aa_length": 767,
"cds_start": 1717,
"cds_end": null,
"cds_length": 2304,
"cdna_start": 2007,
"cdna_end": null,
"cdna_length": 3156,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD3",
"gene_hgnc_id": 470,
"hgvs_c": "c.1240C>T",
"hgvs_p": "p.Arg414Cys",
"transcript": "NM_001172431.2",
"protein_id": "NP_001165902.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 608,
"cds_start": 1240,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 1645,
"cdna_end": null,
"cdna_length": 3927,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD3",
"gene_hgnc_id": 470,
"hgvs_c": "c.1240C>T",
"hgvs_p": "p.Arg414Cys",
"transcript": "ENST00000444303.6",
"protein_id": "ENSP00000396000.2",
"transcript_support_level": 2,
"aa_start": 414,
"aa_end": null,
"aa_length": 608,
"cds_start": 1240,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 1712,
"cdna_end": null,
"cdna_length": 3994,
"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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD3",
"gene_hgnc_id": 470,
"hgvs_c": "n.61C>T",
"hgvs_p": null,
"transcript": "ENST00000529744.1",
"protein_id": "ENSP00000434608.1",
"transcript_support_level": 5,
"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": 593,
"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": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD3",
"gene_hgnc_id": 470,
"hgvs_c": "n.1717C>T",
"hgvs_p": null,
"transcript": "ENST00000529834.5",
"protein_id": "ENSP00000435382.1",
"transcript_support_level": 2,
"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": 2248,
"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": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD3",
"gene_hgnc_id": 470,
"hgvs_c": "n.308C>T",
"hgvs_p": null,
"transcript": "ENST00000530864.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 717,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AMPD3",
"gene_hgnc_id": 470,
"dbsnp": "rs3741040",
"frequency_reference_population": 0.0002446969,
"hom_count_reference_population": 3,
"allele_count_reference_population": 395,
"gnomad_exomes_af": 0.000254466,
"gnomad_genomes_af": 0.000150962,
"gnomad_exomes_ac": 372,
"gnomad_genomes_ac": 23,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.14089658856391907,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.849,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7804,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.36,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.468,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3,PP5_Moderate,BP4,BS2_Supporting",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 2,
"pathogenic_score": 3,
"criteria": [
"PP3",
"PP5_Moderate",
"BP4",
"BS2_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000396553.7",
"gene_symbol": "AMPD3",
"hgnc_id": 470,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1717C>T",
"hgvs_p": "p.Arg573Cys"
}
],
"clinvar_disease": "AMPD3-related disorder,Erythrocyte AMP deaminase deficiency",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Erythrocyte AMP deaminase deficiency|AMPD3-related disorder",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}