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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: 3-46897936-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=46897936&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 46897936,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000449590.6",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.395C>T",
"hgvs_p": "p.Pro132Leu",
"transcript": "NM_000316.3",
"protein_id": "NP_000307.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 593,
"cds_start": 395,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 623,
"cdna_end": null,
"cdna_length": 2153,
"mane_select": "ENST00000449590.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.395C>T",
"hgvs_p": "p.Pro132Leu",
"transcript": "ENST00000449590.6",
"protein_id": "ENSP00000402723.1",
"transcript_support_level": 1,
"aa_start": 132,
"aa_end": null,
"aa_length": 593,
"cds_start": 395,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 623,
"cdna_end": null,
"cdna_length": 2153,
"mane_select": "NM_000316.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.395C>T",
"hgvs_p": "p.Pro132Leu",
"transcript": "ENST00000313049.9",
"protein_id": "ENSP00000321999.4",
"transcript_support_level": 1,
"aa_start": 132,
"aa_end": null,
"aa_length": 593,
"cds_start": 395,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 598,
"cdna_end": null,
"cdna_length": 2123,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.395C>T",
"hgvs_p": "p.Pro132Leu",
"transcript": "ENST00000430002.6",
"protein_id": "ENSP00000413774.2",
"transcript_support_level": 1,
"aa_start": 132,
"aa_end": null,
"aa_length": 593,
"cds_start": 395,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 461,
"cdna_end": null,
"cdna_length": 1947,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.395C>T",
"hgvs_p": "p.Pro132Leu",
"transcript": "NM_001184744.1",
"protein_id": "NP_001171673.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 593,
"cds_start": 395,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 461,
"cdna_end": null,
"cdna_length": 1991,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.395C>T",
"hgvs_p": "p.Pro132Leu",
"transcript": "ENST00000418619.5",
"protein_id": "ENSP00000411424.1",
"transcript_support_level": 5,
"aa_start": 132,
"aa_end": null,
"aa_length": 593,
"cds_start": 395,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 544,
"cdna_end": null,
"cdna_length": 2070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.395C>T",
"hgvs_p": "p.Pro132Leu",
"transcript": "ENST00000427125.6",
"protein_id": "ENSP00000400977.2",
"transcript_support_level": 5,
"aa_start": 132,
"aa_end": null,
"aa_length": 526,
"cds_start": 395,
"cds_end": null,
"cds_length": 1581,
"cdna_start": 728,
"cdna_end": null,
"cdna_length": 1914,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.434C>T",
"hgvs_p": "p.Pro145Leu",
"transcript": "XM_011533967.4",
"protein_id": "XP_011532269.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 606,
"cds_start": 434,
"cds_end": null,
"cds_length": 1821,
"cdna_start": 662,
"cdna_end": null,
"cdna_length": 2192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.434C>T",
"hgvs_p": "p.Pro145Leu",
"transcript": "XM_017006932.3",
"protein_id": "XP_016862421.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 606,
"cds_start": 434,
"cds_end": null,
"cds_length": 1821,
"cdna_start": 690,
"cdna_end": null,
"cdna_length": 2220,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.434C>T",
"hgvs_p": "p.Pro145Leu",
"transcript": "XM_047448632.1",
"protein_id": "XP_047304588.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 606,
"cds_start": 434,
"cds_end": null,
"cds_length": 1821,
"cdna_start": 572,
"cdna_end": null,
"cdna_length": 2102,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.416C>T",
"hgvs_p": "p.Pro139Leu",
"transcript": "XM_011533968.3",
"protein_id": "XP_011532270.1",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 600,
"cds_start": 416,
"cds_end": null,
"cds_length": 1803,
"cdna_start": 539,
"cdna_end": null,
"cdna_length": 2069,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.434C>T",
"hgvs_p": "p.Pro145Leu",
"transcript": "XM_017006934.2",
"protein_id": "XP_016862423.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 516,
"cds_start": 434,
"cds_end": null,
"cds_length": 1551,
"cdna_start": 662,
"cdna_end": null,
"cdna_length": 2188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "c.395C>T",
"hgvs_p": "p.Pro132Leu",
"transcript": "XM_047448633.1",
"protein_id": "XP_047304589.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 503,
"cds_start": 395,
"cds_end": null,
"cds_length": 1512,
"cdna_start": 623,
"cdna_end": null,
"cdna_length": 2149,
"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": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "n.395C>T",
"hgvs_p": null,
"transcript": "ENST00000428220.1",
"protein_id": "ENSP00000389811.1",
"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": 2063,
"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": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"hgvs_c": "n.415C>T",
"hgvs_p": null,
"transcript": "ENST00000490109.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 731,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000308167",
"gene_hgnc_id": null,
"hgvs_c": "n.159+763G>A",
"hgvs_p": null,
"transcript": "ENST00000832121.1",
"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": 352,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTH1R",
"gene_hgnc_id": 9608,
"dbsnp": "rs121434599",
"frequency_reference_population": 0.0000034203517,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000342035,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.991469144821167,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.885,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.945,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.35,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.45,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000449590.6",
"gene_symbol": "PTH1R",
"hgnc_id": 9608,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.395C>T",
"hgvs_p": "p.Pro132Leu"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000832121.1",
"gene_symbol": "ENSG00000308167",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.159+763G>A",
"hgvs_p": null
}
],
"clinvar_disease": " Jansen type,Chondrodysplasia Blomstrand type,Eiken syndrome,Metaphyseal chondrodysplasia,Primary failure of tooth eruption",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Chondrodysplasia Blomstrand type|Metaphyseal chondrodysplasia, Jansen type;Eiken syndrome;Chondrodysplasia Blomstrand type;Primary failure of tooth eruption",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}