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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: 2-126656303-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=126656303&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 126656303,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000259254.9",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYPC",
"gene_hgnc_id": 4704,
"hgvs_c": "c.40C>T",
"hgvs_p": "p.Leu14Phe",
"transcript": "NM_002101.5",
"protein_id": "NP_002092.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 128,
"cds_start": 40,
"cds_end": null,
"cds_length": 387,
"cdna_start": 146,
"cdna_end": null,
"cdna_length": 1018,
"mane_select": "ENST00000259254.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYPC",
"gene_hgnc_id": 4704,
"hgvs_c": "c.40C>T",
"hgvs_p": "p.Leu14Phe",
"transcript": "ENST00000259254.9",
"protein_id": "ENSP00000259254.4",
"transcript_support_level": 1,
"aa_start": 14,
"aa_end": null,
"aa_length": 128,
"cds_start": 40,
"cds_end": null,
"cds_length": 387,
"cdna_start": 146,
"cdna_end": null,
"cdna_length": 1018,
"mane_select": "NM_002101.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYPC",
"gene_hgnc_id": 4704,
"hgvs_c": "c.40C>T",
"hgvs_p": "p.Leu14Phe",
"transcript": "ENST00000409836.3",
"protein_id": "ENSP00000386904.3",
"transcript_support_level": 1,
"aa_start": 14,
"aa_end": null,
"aa_length": 109,
"cds_start": 40,
"cds_end": null,
"cds_length": 330,
"cdna_start": 120,
"cdna_end": null,
"cdna_length": 932,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYPC",
"gene_hgnc_id": 4704,
"hgvs_c": "c.-842C>T",
"hgvs_p": null,
"transcript": "ENST00000356887.12",
"protein_id": "ENSP00000349354.7",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 107,
"cds_start": -4,
"cds_end": null,
"cds_length": 324,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1805,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYPC",
"gene_hgnc_id": 4704,
"hgvs_c": "c.40C>T",
"hgvs_p": "p.Leu14Phe",
"transcript": "NM_016815.4",
"protein_id": "NP_058131.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 109,
"cds_start": 40,
"cds_end": null,
"cds_length": 330,
"cdna_start": 146,
"cdna_end": null,
"cdna_length": 961,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYPC",
"gene_hgnc_id": 4704,
"hgvs_c": "n.162C>T",
"hgvs_p": null,
"transcript": "ENST00000459787.1",
"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": 758,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYPC",
"gene_hgnc_id": 4704,
"hgvs_c": "n.171C>T",
"hgvs_p": null,
"transcript": "ENST00000484700.2",
"protein_id": null,
"transcript_support_level": 5,
"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": 1341,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYPC",
"gene_hgnc_id": 4704,
"hgvs_c": "c.-842C>T",
"hgvs_p": null,
"transcript": "NM_001256584.2",
"protein_id": "NP_001243513.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 107,
"cds_start": -4,
"cds_end": null,
"cds_length": 324,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1836,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYPC",
"gene_hgnc_id": 4704,
"hgvs_c": "c.-25C>T",
"hgvs_p": null,
"transcript": "XM_047444034.1",
"protein_id": "XP_047299990.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 146,
"cds_start": -4,
"cds_end": null,
"cds_length": 441,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1136,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYPC",
"gene_hgnc_id": 4704,
"hgvs_c": "c.-290C>T",
"hgvs_p": null,
"transcript": "XM_047444035.1",
"protein_id": "XP_047299991.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 122,
"cds_start": -4,
"cds_end": null,
"cds_length": 369,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1329,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GYPC",
"gene_hgnc_id": 4704,
"dbsnp": "rs121912761",
"frequency_reference_population": 0.00001820915,
"hom_count_reference_population": 0,
"allele_count_reference_population": 29,
"gnomad_exomes_af": 0.0000173557,
"gnomad_genomes_af": 0.0000262888,
"gnomad_exomes_ac": 25,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3591671884059906,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.042,
"revel_prediction": "Benign",
"alphamissense_score": 0.0723,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.72,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.605,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000259254.9",
"gene_symbol": "GYPC",
"hgnc_id": 4704,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.40C>T",
"hgvs_p": "p.Leu14Phe"
}
],
"clinvar_disease": " Gerbich system,Blood group",
"clinvar_classification": "Affects",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Blood group, Gerbich system",
"pathogenicity_classification_combined": "Affects",
"custom_annotations": null
}
],
"message": null
}