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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: 5-74721774-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=74721774&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 74721774,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000296805.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.2221A>C",
"hgvs_p": "p.Thr741Pro",
"transcript": "NM_032380.5",
"protein_id": "NP_115756.2",
"transcript_support_level": null,
"aa_start": 741,
"aa_end": null,
"aa_length": 779,
"cds_start": 2221,
"cds_end": null,
"cds_length": 2340,
"cdna_start": 2425,
"cdna_end": null,
"cdna_length": 2993,
"mane_select": "ENST00000296805.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.2221A>C",
"hgvs_p": "p.Thr741Pro",
"transcript": "ENST00000296805.8",
"protein_id": "ENSP00000296805.3",
"transcript_support_level": 1,
"aa_start": 741,
"aa_end": null,
"aa_length": 779,
"cds_start": 2221,
"cds_end": null,
"cds_length": 2340,
"cdna_start": 2425,
"cdna_end": null,
"cdna_length": 2993,
"mane_select": "NM_032380.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.2221A>C",
"hgvs_p": "p.Thr741Pro",
"transcript": "ENST00000509430.5",
"protein_id": "ENSP00000427004.1",
"transcript_support_level": 1,
"aa_start": 741,
"aa_end": null,
"aa_length": 779,
"cds_start": 2221,
"cds_end": null,
"cds_length": 2340,
"cdna_start": 2531,
"cdna_end": null,
"cdna_length": 3047,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.2080A>C",
"hgvs_p": "p.Thr694Pro",
"transcript": "ENST00000345239.6",
"protein_id": "ENSP00000296804.3",
"transcript_support_level": 1,
"aa_start": 694,
"aa_end": null,
"aa_length": 732,
"cds_start": 2080,
"cds_end": null,
"cds_length": 2199,
"cdna_start": 2288,
"cdna_end": null,
"cdna_length": 2856,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.2317A>C",
"hgvs_p": "p.Thr773Pro",
"transcript": "NM_001281302.2",
"protein_id": "NP_001268231.1",
"transcript_support_level": null,
"aa_start": 773,
"aa_end": null,
"aa_length": 811,
"cds_start": 2317,
"cds_end": null,
"cds_length": 2436,
"cdna_start": 2543,
"cdna_end": null,
"cdna_length": 3111,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.2080A>C",
"hgvs_p": "p.Thr694Pro",
"transcript": "NM_170691.3",
"protein_id": "NP_733792.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 732,
"cds_start": 2080,
"cds_end": null,
"cds_length": 2199,
"cdna_start": 2284,
"cdna_end": null,
"cdna_length": 2852,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.2221A>C",
"hgvs_p": "p.Thr741Pro",
"transcript": "XM_017009986.2",
"protein_id": "XP_016865475.1",
"transcript_support_level": null,
"aa_start": 741,
"aa_end": null,
"aa_length": 779,
"cds_start": 2221,
"cds_end": null,
"cds_length": 2340,
"cdna_start": 2751,
"cdna_end": null,
"cdna_length": 3319,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.2221A>C",
"hgvs_p": "p.Thr741Pro",
"transcript": "XM_047417833.1",
"protein_id": "XP_047273789.1",
"transcript_support_level": null,
"aa_start": 741,
"aa_end": null,
"aa_length": 779,
"cds_start": 2221,
"cds_end": null,
"cds_length": 2340,
"cdna_start": 2863,
"cdna_end": null,
"cdna_length": 3431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.2080A>C",
"hgvs_p": "p.Thr694Pro",
"transcript": "XM_047417834.1",
"protein_id": "XP_047273790.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 732,
"cds_start": 2080,
"cds_end": null,
"cds_length": 2199,
"cdna_start": 2722,
"cdna_end": null,
"cdna_length": 3290,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.2080A>C",
"hgvs_p": "p.Thr694Pro",
"transcript": "XM_047417835.1",
"protein_id": "XP_047273791.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 732,
"cds_start": 2080,
"cds_end": null,
"cds_length": 2199,
"cdna_start": 2610,
"cdna_end": null,
"cdna_length": 3178,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "n.624A>C",
"hgvs_p": null,
"transcript": "ENST00000515125.5",
"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": 1125,
"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": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "n.2286A>C",
"hgvs_p": null,
"transcript": "NR_104006.2",
"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": 2854,
"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": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "n.*97+338T>G",
"hgvs_p": null,
"transcript": "ENST00000503312.5",
"protein_id": "ENSP00000426384.1",
"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": 756,
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "n.*97+338T>G",
"hgvs_p": null,
"transcript": "ENST00000505859.1",
"protein_id": "ENSP00000424550.1",
"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": 604,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "n.380+338T>G",
"hgvs_p": null,
"transcript": "ENST00000513867.1",
"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": 711,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"dbsnp": "rs773006254",
"frequency_reference_population": 0.0000012411398,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 6.85296e-7,
"gnomad_genomes_af": 0.00000657039,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.932070255279541,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.776,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.391,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.3,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.67,
"phylop100way_prediction": "Pathogenic",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000296805.8",
"gene_symbol": "GFM2",
"hgnc_id": 29682,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2221A>C",
"hgvs_p": "p.Thr741Pro"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000513867.1",
"gene_symbol": "HEXB",
"hgnc_id": 4879,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.380+338T>G",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}