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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: 2-113220116-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=113220116&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 113220116,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000429538.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.1252C>T",
"hgvs_p": "p.Arg418Cys",
"transcript": "NM_003466.4",
"protein_id": "NP_003457.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 450,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1353,
"cdna_start": 1418,
"cdna_end": null,
"cdna_length": 4055,
"mane_select": "ENST00000429538.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.1252C>T",
"hgvs_p": "p.Arg418Cys",
"transcript": "ENST00000429538.8",
"protein_id": "ENSP00000395498.3",
"transcript_support_level": 1,
"aa_start": 418,
"aa_end": null,
"aa_length": 450,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1353,
"cdna_start": 1418,
"cdna_end": null,
"cdna_length": 4055,
"mane_select": "NM_003466.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.1252C>T",
"hgvs_p": "p.Arg418Cys",
"transcript": "ENST00000263334.9",
"protein_id": "ENSP00000263334.6",
"transcript_support_level": 1,
"aa_start": 418,
"aa_end": null,
"aa_length": 450,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1353,
"cdna_start": 1515,
"cdna_end": null,
"cdna_length": 4152,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.1173C>T",
"hgvs_p": "p.Gly391Gly",
"transcript": "ENST00000348715.9",
"protein_id": "ENSP00000314750.5",
"transcript_support_level": 1,
"aa_start": 391,
"aa_end": null,
"aa_length": 398,
"cds_start": 1173,
"cds_end": null,
"cds_length": 1197,
"cdna_start": 1329,
"cdna_end": null,
"cdna_length": 3966,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.942C>T",
"hgvs_p": "p.Gly314Gly",
"transcript": "ENST00000263335.11",
"protein_id": "ENSP00000263335.7",
"transcript_support_level": 1,
"aa_start": 314,
"aa_end": null,
"aa_length": 321,
"cds_start": 942,
"cds_end": null,
"cds_length": 966,
"cdna_start": 1098,
"cdna_end": null,
"cdna_length": 3735,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.840C>T",
"hgvs_p": "p.Gly280Gly",
"transcript": "ENST00000397647.7",
"protein_id": "ENSP00000380768.3",
"transcript_support_level": 1,
"aa_start": 280,
"aa_end": null,
"aa_length": 287,
"cds_start": 840,
"cds_end": null,
"cds_length": 864,
"cdna_start": 996,
"cdna_end": null,
"cdna_length": 3633,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "n.362C>T",
"hgvs_p": null,
"transcript": "ENST00000480684.1",
"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": 527,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PAX8-AS1",
"gene_hgnc_id": 49271,
"hgvs_c": "n.305+3754G>A",
"hgvs_p": null,
"transcript": "ENST00000456685.5",
"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": 1207,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.1252C>T",
"hgvs_p": "p.Arg418Cys",
"transcript": "ENST00000681162.1",
"protein_id": "ENSP00000505425.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 453,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1362,
"cdna_start": 1418,
"cdna_end": null,
"cdna_length": 4036,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.1063C>T",
"hgvs_p": "p.Arg355Cys",
"transcript": "ENST00000468980.4",
"protein_id": "ENSP00000451240.2",
"transcript_support_level": 3,
"aa_start": 355,
"aa_end": null,
"aa_length": 387,
"cds_start": 1063,
"cds_end": null,
"cds_length": 1164,
"cdna_start": 1086,
"cdna_end": null,
"cdna_length": 2344,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.157C>T",
"hgvs_p": "p.Arg53Cys",
"transcript": "ENST00000497038.6",
"protein_id": "ENSP00000451618.3",
"transcript_support_level": 5,
"aa_start": 53,
"aa_end": null,
"aa_length": 85,
"cds_start": 157,
"cds_end": null,
"cds_length": 258,
"cdna_start": 704,
"cdna_end": null,
"cdna_length": 816,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.1173C>T",
"hgvs_p": "p.Gly391Gly",
"transcript": "NM_013952.4",
"protein_id": "NP_039246.1",
"transcript_support_level": null,
"aa_start": 391,
"aa_end": null,
"aa_length": 398,
"cds_start": 1173,
"cds_end": null,
"cds_length": 1197,
"cdna_start": 1339,
"cdna_end": null,
"cdna_length": 3976,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.942C>T",
"hgvs_p": "p.Gly314Gly",
"transcript": "NM_013953.4",
"protein_id": "NP_039247.1",
"transcript_support_level": null,
"aa_start": 314,
"aa_end": null,
"aa_length": 321,
"cds_start": 942,
"cds_end": null,
"cds_length": 966,
"cdna_start": 1108,
"cdna_end": null,
"cdna_length": 3745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.840C>T",
"hgvs_p": "p.Gly280Gly",
"transcript": "NM_013992.4",
"protein_id": "NP_054698.1",
"transcript_support_level": null,
"aa_start": 280,
"aa_end": null,
"aa_length": 287,
"cds_start": 840,
"cds_end": null,
"cds_length": 864,
"cdna_start": 1006,
"cdna_end": null,
"cdna_length": 3643,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.270C>T",
"hgvs_p": "p.Gly90Gly",
"transcript": "ENST00000465084.1",
"protein_id": "ENSP00000452547.1",
"transcript_support_level": 2,
"aa_start": 90,
"aa_end": null,
"aa_length": 97,
"cds_start": 270,
"cds_end": null,
"cds_length": 294,
"cdna_start": 271,
"cdna_end": null,
"cdna_length": 656,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PAX8-AS1",
"gene_hgnc_id": 49271,
"hgvs_c": "n.200-5486G>A",
"hgvs_p": null,
"transcript": "ENST00000662215.1",
"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": 818,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PAX8-AS1",
"gene_hgnc_id": 49271,
"hgvs_c": "n.142-5486G>A",
"hgvs_p": null,
"transcript": "ENST00000777999.1",
"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": 284,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"dbsnp": "rs1048942",
"frequency_reference_population": 0.00002726724,
"hom_count_reference_population": 0,
"allele_count_reference_population": 44,
"gnomad_exomes_af": 0.0000253165,
"gnomad_genomes_af": 0.0000460042,
"gnomad_exomes_ac": 37,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7593284249305725,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.799,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6302,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.306,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000429538.8",
"gene_symbol": "PAX8",
"hgnc_id": 8622,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1252C>T",
"hgvs_p": "p.Arg418Cys"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000456685.5",
"gene_symbol": "PAX8-AS1",
"hgnc_id": 49271,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.305+3754G>A",
"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
}