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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: 1-31633242-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=31633242&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 31633242,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_012392.4",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "c.398A>C",
"hgvs_p": "p.Tyr133Ser",
"transcript": "NM_012392.4",
"protein_id": "NP_036524.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 284,
"cds_start": 398,
"cds_end": null,
"cds_length": 855,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000373703.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_012392.4"
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "c.398A>C",
"hgvs_p": "p.Tyr133Ser",
"transcript": "ENST00000373703.5",
"protein_id": "ENSP00000362807.4",
"transcript_support_level": 1,
"aa_start": 133,
"aa_end": null,
"aa_length": 284,
"cds_start": 398,
"cds_end": null,
"cds_length": 855,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_012392.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000373703.5"
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "c.398A>C",
"hgvs_p": "p.Tyr133Ser",
"transcript": "ENST00000859308.1",
"protein_id": "ENSP00000529367.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 236,
"cds_start": 398,
"cds_end": null,
"cds_length": 711,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000859308.1"
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "c.188A>C",
"hgvs_p": "p.Tyr63Ser",
"transcript": "NM_001359651.2",
"protein_id": "NP_001346580.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 214,
"cds_start": 188,
"cds_end": null,
"cds_length": 645,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001359651.2"
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "c.140A>C",
"hgvs_p": "p.Tyr47Ser",
"transcript": "ENST00000859307.1",
"protein_id": "ENSP00000529366.1",
"transcript_support_level": null,
"aa_start": 47,
"aa_end": null,
"aa_length": 198,
"cds_start": 140,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000859307.1"
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "c.383A>C",
"hgvs_p": "p.Tyr128Ser",
"transcript": "XM_011541745.2",
"protein_id": "XP_011540047.1",
"transcript_support_level": null,
"aa_start": 128,
"aa_end": null,
"aa_length": 279,
"cds_start": 383,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541745.2"
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "c.188A>C",
"hgvs_p": "p.Tyr63Ser",
"transcript": "XM_011541746.3",
"protein_id": "XP_011540048.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 214,
"cds_start": 188,
"cds_end": null,
"cds_length": 645,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541746.3"
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "c.188A>C",
"hgvs_p": "p.Tyr63Ser",
"transcript": "XM_011541747.2",
"protein_id": "XP_011540049.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 214,
"cds_start": 188,
"cds_end": null,
"cds_length": 645,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541747.2"
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "c.188A>C",
"hgvs_p": "p.Tyr63Ser",
"transcript": "XM_017001680.2",
"protein_id": "XP_016857169.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 214,
"cds_start": 188,
"cds_end": null,
"cds_length": 645,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001680.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCRTR1",
"gene_hgnc_id": 4848,
"hgvs_c": "c.*724T>G",
"hgvs_p": null,
"transcript": "XM_017001107.2",
"protein_id": "XP_016856596.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 389,
"cds_start": null,
"cds_end": null,
"cds_length": 1170,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001107.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "c.326-604A>C",
"hgvs_p": null,
"transcript": "ENST00000911438.1",
"protein_id": "ENSP00000581497.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 232,
"cds_start": null,
"cds_end": null,
"cds_length": 699,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911438.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "c.325+1980A>C",
"hgvs_p": null,
"transcript": "ENST00000966434.1",
"protein_id": "ENSP00000636493.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 184,
"cds_start": null,
"cds_end": null,
"cds_length": 555,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000966434.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "c.68-604A>C",
"hgvs_p": null,
"transcript": "ENST00000859309.1",
"protein_id": "ENSP00000529368.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 146,
"cds_start": null,
"cds_end": null,
"cds_length": 441,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000859309.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "n.112A>C",
"hgvs_p": null,
"transcript": "ENST00000461006.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000461006.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "n.129A>C",
"hgvs_p": null,
"transcript": "ENST00000478502.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000478502.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "n.584A>C",
"hgvs_p": null,
"transcript": "ENST00000489164.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000489164.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "n.853A>C",
"hgvs_p": null,
"transcript": "ENST00000492061.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000492061.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "n.740A>C",
"hgvs_p": null,
"transcript": "ENST00000496805.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000496805.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "n.109A>C",
"hgvs_p": null,
"transcript": "NR_033686.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_033686.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "n.*33A>C",
"hgvs_p": null,
"transcript": "ENST00000471219.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000471219.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"hgvs_c": "n.*22A>C",
"hgvs_p": null,
"transcript": "ENST00000472443.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000472443.1"
}
],
"gene_symbol": "PEF1",
"gene_hgnc_id": 30009,
"dbsnp": "rs781584359",
"frequency_reference_population": 6.841087e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84109e-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": 0.3435499668121338,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.51,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1597,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.639,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PM2,BP4",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 1,
"pathogenic_score": 4,
"criteria": [
"PM1",
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_012392.4",
"gene_symbol": "PEF1",
"hgnc_id": 30009,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.398A>C",
"hgvs_p": "p.Tyr133Ser"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "XM_017001107.2",
"gene_symbol": "HCRTR1",
"hgnc_id": 4848,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*724T>G",
"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
}