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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: 7-127613497-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=127613497&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 127613497,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000639438.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX4",
"gene_hgnc_id": 8618,
"hgvs_c": "c.598C>A",
"hgvs_p": "p.Arg200Ser",
"transcript": "NM_001366110.1",
"protein_id": "NP_001353039.1",
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 351,
"cds_start": 598,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 1004,
"cdna_end": null,
"cdna_length": 2234,
"mane_select": "ENST00000639438.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX4",
"gene_hgnc_id": 8618,
"hgvs_c": "c.598C>A",
"hgvs_p": "p.Arg200Ser",
"transcript": "ENST00000639438.3",
"protein_id": "ENSP00000491782.1",
"transcript_support_level": 5,
"aa_start": 200,
"aa_end": null,
"aa_length": 351,
"cds_start": 598,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 1004,
"cdna_end": null,
"cdna_length": 2234,
"mane_select": "NM_001366110.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX4",
"gene_hgnc_id": 8618,
"hgvs_c": "c.598C>A",
"hgvs_p": "p.Arg200Ser",
"transcript": "ENST00000378740.6",
"protein_id": "ENSP00000368014.4",
"transcript_support_level": 1,
"aa_start": 200,
"aa_end": null,
"aa_length": 348,
"cds_start": 598,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 598,
"cdna_end": null,
"cdna_length": 1088,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX4",
"gene_hgnc_id": 8618,
"hgvs_c": "c.574C>A",
"hgvs_p": "p.Arg192Ser",
"transcript": "ENST00000341640.6",
"protein_id": "ENSP00000339906.2",
"transcript_support_level": 1,
"aa_start": 192,
"aa_end": null,
"aa_length": 343,
"cds_start": 574,
"cds_end": null,
"cds_length": 1032,
"cdna_start": 780,
"cdna_end": null,
"cdna_length": 2010,
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX4",
"gene_hgnc_id": 8618,
"hgvs_c": "n.1029C>A",
"hgvs_p": null,
"transcript": "ENST00000463946.5",
"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": 1613,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX4",
"gene_hgnc_id": 8618,
"hgvs_c": "n.568C>A",
"hgvs_p": null,
"transcript": "ENST00000477423.1",
"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": 935,
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX4",
"gene_hgnc_id": 8618,
"hgvs_c": "n.1029C>A",
"hgvs_p": null,
"transcript": "ENST00000483494.5",
"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": 1565,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAX4",
"gene_hgnc_id": 8618,
"hgvs_c": "c.598C>A",
"hgvs_p": "p.Arg200Ser",
"transcript": "NM_001366111.1",
"protein_id": "NP_001353040.1",
"transcript_support_level": null,
"aa_start": 200,
"aa_end": null,
"aa_length": 348,
"cds_start": 598,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 697,
"cdna_end": null,
"cdna_length": 1706,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PAX4",
"gene_hgnc_id": 8618,
"dbsnp": "rs3824004",
"frequency_reference_population": 0.00096087484,
"hom_count_reference_population": 23,
"allele_count_reference_population": 1551,
"gnomad_exomes_af": 0.000942619,
"gnomad_genomes_af": 0.00113614,
"gnomad_exomes_ac": 1378,
"gnomad_genomes_ac": 173,
"gnomad_exomes_homalt": 22,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.010282635688781738,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.913,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9487,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.5,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.446,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.05,
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "PP3,BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 20,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000639438.3",
"gene_symbol": "PAX4",
"hgnc_id": 8618,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AD",
"hgvs_c": "c.598C>A",
"hgvs_p": "p.Arg200Ser"
}
],
"clinvar_disease": "Maturity onset diabetes mellitus in young,Monogenic diabetes,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:5",
"phenotype_combined": "Maturity onset diabetes mellitus in young|Monogenic diabetes|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}