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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: 2-113216207-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=113216207&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 113216207,
"ref": "T",
"alt": "C",
"effect": "3_prime_UTR_variant",
"transcript": "ENST00000429538.8",
"consequences": [
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8-AS1",
"gene_hgnc_id": 49271,
"hgvs_c": "n.150T>C",
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.*2326A>G",
"hgvs_p": null,
"transcript": "NM_003466.4",
"protein_id": "NP_003457.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 450,
"cds_start": -4,
"cds_end": null,
"cds_length": 1353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4055,
"mane_select": "ENST00000429538.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.*2326A>G",
"hgvs_p": null,
"transcript": "ENST00000429538.8",
"protein_id": "ENSP00000395498.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 450,
"cds_start": -4,
"cds_end": null,
"cds_length": 1353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4055,
"mane_select": "NM_003466.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.*2326A>G",
"hgvs_p": null,
"transcript": "ENST00000263334.9",
"protein_id": "ENSP00000263334.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 450,
"cds_start": -4,
"cds_end": null,
"cds_length": 1353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4152,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.*2403A>G",
"hgvs_p": null,
"transcript": "ENST00000348715.9",
"protein_id": "ENSP00000314750.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 398,
"cds_start": -4,
"cds_end": null,
"cds_length": 1197,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3966,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.*2403A>G",
"hgvs_p": null,
"transcript": "ENST00000263335.11",
"protein_id": "ENSP00000263335.7",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 321,
"cds_start": -4,
"cds_end": null,
"cds_length": 966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3735,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.*2403A>G",
"hgvs_p": null,
"transcript": "ENST00000397647.7",
"protein_id": "ENSP00000380768.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 287,
"cds_start": -4,
"cds_end": null,
"cds_length": 864,
"cdna_start": null,
"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": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.*2298A>G",
"hgvs_p": null,
"transcript": "ENST00000681162.1",
"protein_id": "ENSP00000505425.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 453,
"cds_start": -4,
"cds_end": null,
"cds_length": 1362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4036,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.*2403A>G",
"hgvs_p": null,
"transcript": "NM_013952.4",
"protein_id": "NP_039246.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 398,
"cds_start": -4,
"cds_end": null,
"cds_length": 1197,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3976,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.*2403A>G",
"hgvs_p": null,
"transcript": "NM_013953.4",
"protein_id": "NP_039247.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 321,
"cds_start": -4,
"cds_end": null,
"cds_length": 966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX8",
"gene_hgnc_id": 8622,
"hgvs_c": "c.*2403A>G",
"hgvs_p": null,
"transcript": "NM_013992.4",
"protein_id": "NP_054698.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 287,
"cds_start": -4,
"cds_end": null,
"cds_length": 864,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3643,
"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.199+4588T>C",
"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.141+4588T>C",
"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": "rs886054783",
"frequency_reference_population": 0.000006570475,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000657047,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8500000238418579,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.85,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.448,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.08,
"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": "ENST00000429538.8",
"gene_symbol": "PAX8",
"hgnc_id": 8622,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.*2326A>G",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000456685.5",
"gene_symbol": "PAX8-AS1",
"hgnc_id": 49271,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.150T>C",
"hgvs_p": null
}
],
"clinvar_disease": " 2, congenital, nongoitrous,Hypothyroidism",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Hypothyroidism, congenital, nongoitrous, 2",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}