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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: 3-10098431-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=10098431&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 10098431,
"ref": "G",
"alt": "A",
"effect": "intron_variant",
"transcript": "ENST00000675286.1",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": 42,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.4186-289G>A",
"hgvs_p": null,
"transcript": "NM_001018115.3",
"protein_id": "NP_001018125.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1451,
"cds_start": -4,
"cds_end": null,
"cds_length": 4356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5096,
"mane_select": "ENST00000675286.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": 42,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.4186-289G>A",
"hgvs_p": null,
"transcript": "ENST00000675286.1",
"protein_id": "ENSP00000502379.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1451,
"cds_start": -4,
"cds_end": null,
"cds_length": 4356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5096,
"mane_select": "NM_001018115.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": 42,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.4186-289G>A",
"hgvs_p": null,
"transcript": "ENST00000287647.7",
"protein_id": "ENSP00000287647.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1471,
"cds_start": -4,
"cds_end": null,
"cds_length": 4416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5219,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": 42,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.4186-289G>A",
"hgvs_p": null,
"transcript": "ENST00000419585.5",
"protein_id": "ENSP00000398754.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1451,
"cds_start": -4,
"cds_end": null,
"cds_length": 4356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5185,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "FANCD2OS",
"gene_hgnc_id": 28623,
"hgvs_c": "c.*43+5767C>T",
"hgvs_p": null,
"transcript": "ENST00000524279.1",
"protein_id": "ENSP00000429663.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 177,
"cds_start": -4,
"cds_end": null,
"cds_length": 534,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1014,
"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": 27,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "n.*342-289G>A",
"hgvs_p": null,
"transcript": "ENST00000421731.5",
"protein_id": "ENSP00000389936.1",
"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": 3425,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": 42,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.4186-289G>A",
"hgvs_p": null,
"transcript": "NM_033084.6",
"protein_id": "NP_149075.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1471,
"cds_start": -4,
"cds_end": null,
"cds_length": 4416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4879,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": 41,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.4147-289G>A",
"hgvs_p": null,
"transcript": "NM_001374254.1",
"protein_id": "NP_001361183.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1458,
"cds_start": -4,
"cds_end": null,
"cds_length": 4377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4840,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": 42,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.4186-289G>A",
"hgvs_p": null,
"transcript": "NM_001319984.2",
"protein_id": "NP_001306913.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1451,
"cds_start": -4,
"cds_end": null,
"cds_length": 4356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5249,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": 41,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.4075-289G>A",
"hgvs_p": null,
"transcript": "NM_001374253.1",
"protein_id": "NP_001361182.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1414,
"cds_start": -4,
"cds_end": null,
"cds_length": 4245,
"cdna_start": null,
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"cdna_length": 4985,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": 41,
"intron_rank_end": null,
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"hgvs_c": "c.4075-289G>A",
"hgvs_p": null,
"transcript": "ENST00000676013.1",
"protein_id": "ENSP00000501999.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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"feature": null
},
{
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"canonical": false,
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"strand": false,
"consequences": [
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],
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"exon_count": 3,
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"gene_symbol": "FANCD2OS",
"gene_hgnc_id": 28623,
"hgvs_c": "c.*43+5767C>T",
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"transcript": "NM_173472.2",
"protein_id": "NP_775743.1",
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"cds_start": -4,
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},
{
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"strand": false,
"consequences": [
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],
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"exon_count": 4,
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"gene_symbol": "FANCD2OS",
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"hgvs_c": "n.71-3541C>T",
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"transcript": "ENST00000431315.5",
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},
{
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"strand": true,
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],
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"gene_symbol": "FANCD2",
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"hgvs_c": "n.259-289G>A",
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"transcript": "ENST00000470028.1",
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},
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],
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},
{
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"strand": true,
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],
"exon_rank": null,
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"intron_rank": 29,
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"gene_symbol": "FANCD2",
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},
{
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],
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"gene_symbol": "FANCD2",
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"transcript": "ENST00000683312.1",
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},
{
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],
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"intron_rank": 3,
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"gene_symbol": "FANCD2OS",
"gene_hgnc_id": 28623,
"hgvs_c": "c.*43+5767C>T",
"hgvs_p": null,
"transcript": "XM_047447400.1",
"protein_id": "XP_047303356.1",
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},
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"strand": false,
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],
"exon_rank": null,
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"exon_count": 6,
"intron_rank": 3,
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"gene_symbol": "FANCD2OS",
"gene_hgnc_id": 28623,
"hgvs_c": "n.924-3541C>T",
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},
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],
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},
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],
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},
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],
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"gene_symbol": "FANCD2OS",
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"hgvs_c": "n.827-3541C>T",
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"biotype": null,
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},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "FANCD2OS",
"gene_hgnc_id": 28623,
"hgvs_c": "n.800-3541C>T",
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"transcript": "XR_007095636.1",
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"mane_select": null,
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}
],
"gene_symbol": "FANCD2",
"gene_hgnc_id": 3585,
"dbsnp": "rs2272123",
"frequency_reference_population": 0.20755848,
"hom_count_reference_population": 3963,
"allele_count_reference_population": 31519,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.207558,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 31519,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 3963,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.949999988079071,
"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": -0.95,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.355,
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BA1",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000675286.1",
"gene_symbol": "FANCD2",
"hgnc_id": 3585,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4186-289G>A",
"hgvs_p": null
},
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_173472.2",
"gene_symbol": "FANCD2OS",
"hgnc_id": 28623,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*43+5767C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}