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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: 3-16367271-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=16367271&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 16367271,
"ref": "C",
"alt": "T",
"effect": "intron_variant",
"transcript": "ENST00000334133.9",
"consequences": [
{
"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": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "RFTN1",
"gene_hgnc_id": 30278,
"hgvs_c": "c.1030+2805G>A",
"hgvs_p": null,
"transcript": "NM_015150.2",
"protein_id": "NP_055965.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 578,
"cds_start": -4,
"cds_end": null,
"cds_length": 1737,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2986,
"mane_select": "ENST00000334133.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "RFTN1",
"gene_hgnc_id": 30278,
"hgvs_c": "c.1030+2805G>A",
"hgvs_p": null,
"transcript": "ENST00000334133.9",
"protein_id": "ENSP00000334153.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 578,
"cds_start": -4,
"cds_end": null,
"cds_length": 1737,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2986,
"mane_select": "NM_015150.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "RFTN1",
"gene_hgnc_id": 30278,
"hgvs_c": "c.922+2805G>A",
"hgvs_p": null,
"transcript": "ENST00000432519.5",
"protein_id": "ENSP00000403926.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 542,
"cds_start": -4,
"cds_end": null,
"cds_length": 1629,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2695,
"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": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "RFTN1",
"gene_hgnc_id": 30278,
"hgvs_c": "n.309+2805G>A",
"hgvs_p": null,
"transcript": "ENST00000483671.1",
"protein_id": null,
"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": 1314,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000287377",
"gene_hgnc_id": null,
"hgvs_c": "n.348-2408C>T",
"hgvs_p": null,
"transcript": "ENST00000653928.1",
"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": 1067,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "RFTN1",
"gene_hgnc_id": 30278,
"hgvs_c": "c.1135+2805G>A",
"hgvs_p": null,
"transcript": "XM_047447779.1",
"protein_id": "XP_047303735.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 613,
"cds_start": -4,
"cds_end": null,
"cds_length": 1842,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3009,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "RFTN1",
"gene_hgnc_id": 30278,
"hgvs_c": "c.1030+2805G>A",
"hgvs_p": null,
"transcript": "XM_005264985.2",
"protein_id": "XP_005265042.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 578,
"cds_start": -4,
"cds_end": null,
"cds_length": 1737,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2989,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "RFTN1",
"gene_hgnc_id": 30278,
"hgvs_c": "c.1030+2805G>A",
"hgvs_p": null,
"transcript": "XM_005264986.3",
"protein_id": "XP_005265043.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 578,
"cds_start": -4,
"cds_end": null,
"cds_length": 1737,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2861,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "RFTN1",
"gene_hgnc_id": 30278,
"hgvs_c": "c.1030+2805G>A",
"hgvs_p": null,
"transcript": "XM_006713069.2",
"protein_id": "XP_006713132.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 578,
"cds_start": -4,
"cds_end": null,
"cds_length": 1737,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2864,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "RFTN1",
"gene_hgnc_id": 30278,
"hgvs_c": "c.1030+2805G>A",
"hgvs_p": null,
"transcript": "XM_011533530.2",
"protein_id": "XP_011531832.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 578,
"cds_start": -4,
"cds_end": null,
"cds_length": 1737,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3180,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "RFTN1",
"gene_hgnc_id": 30278,
"hgvs_c": "c.1030+2805G>A",
"hgvs_p": null,
"transcript": "XM_047447780.1",
"protein_id": "XP_047303736.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 578,
"cds_start": -4,
"cds_end": null,
"cds_length": 1737,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3183,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "RFTN1",
"gene_hgnc_id": 30278,
"hgvs_c": "c.1135+2805G>A",
"hgvs_p": null,
"transcript": "XM_047447781.1",
"protein_id": "XP_047303737.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 460,
"cds_start": -4,
"cds_end": null,
"cds_length": 1383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2898,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "RFTN1",
"gene_hgnc_id": 30278,
"hgvs_c": "c.1030+2805G>A",
"hgvs_p": null,
"transcript": "XM_017006007.3",
"protein_id": "XP_016861496.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 425,
"cds_start": -4,
"cds_end": null,
"cds_length": 1278,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2870,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "RFTN1",
"gene_hgnc_id": 30278,
"hgvs_c": "c.1030+2805G>A",
"hgvs_p": null,
"transcript": "XM_047447783.1",
"protein_id": "XP_047303739.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 425,
"cds_start": -4,
"cds_end": null,
"cds_length": 1278,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2873,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RFTN1",
"gene_hgnc_id": 30278,
"dbsnp": "rs689953",
"frequency_reference_population": 0.5259077,
"hom_count_reference_population": 20684,
"allele_count_reference_population": 78477,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.525908,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 78477,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 20684,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6200000047683716,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.156,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000334133.9",
"gene_symbol": "RFTN1",
"hgnc_id": 30278,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1030+2805G>A",
"hgvs_p": null
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000653928.1",
"gene_symbol": "ENSG00000287377",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.348-2408C>T",
"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
}