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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: 16-89783015-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=89783015&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 89783015,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000135.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"hgvs_c": "c.1558G>A",
"hgvs_p": "p.Asp520Asn",
"transcript": "NM_000135.4",
"protein_id": "NP_000126.2",
"transcript_support_level": null,
"aa_start": 520,
"aa_end": null,
"aa_length": 1455,
"cds_start": 1558,
"cds_end": null,
"cds_length": 4368,
"cdna_start": 1590,
"cdna_end": null,
"cdna_length": 5452,
"mane_select": "ENST00000389301.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"hgvs_c": "c.1558G>A",
"hgvs_p": "p.Asp520Asn",
"transcript": "ENST00000389301.8",
"protein_id": "ENSP00000373952.3",
"transcript_support_level": 1,
"aa_start": 520,
"aa_end": null,
"aa_length": 1455,
"cds_start": 1558,
"cds_end": null,
"cds_length": 4368,
"cdna_start": 1590,
"cdna_end": null,
"cdna_length": 5452,
"mane_select": "NM_000135.4",
"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": 16,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"hgvs_c": "n.1558G>A",
"hgvs_p": null,
"transcript": "ENST00000567205.2",
"protein_id": "ENSP00000457027.2",
"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": 2772,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"hgvs_c": "c.1558G>A",
"hgvs_p": "p.Asp520Asn",
"transcript": "ENST00000564475.6",
"protein_id": "ENSP00000454977.2",
"transcript_support_level": 2,
"aa_start": 520,
"aa_end": null,
"aa_length": 1463,
"cds_start": 1558,
"cds_end": null,
"cds_length": 4392,
"cdna_start": 1601,
"cdna_end": null,
"cdna_length": 4686,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"hgvs_c": "c.1558G>A",
"hgvs_p": "p.Asp520Asn",
"transcript": "NM_001286167.3",
"protein_id": "NP_001273096.1",
"transcript_support_level": null,
"aa_start": 520,
"aa_end": null,
"aa_length": 1424,
"cds_start": 1558,
"cds_end": null,
"cds_length": 4275,
"cdna_start": 1590,
"cdna_end": null,
"cdna_length": 5456,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"hgvs_c": "c.1558G>A",
"hgvs_p": "p.Asp520Asn",
"transcript": "ENST00000568369.6",
"protein_id": "ENSP00000456829.1",
"transcript_support_level": 2,
"aa_start": 520,
"aa_end": null,
"aa_length": 1424,
"cds_start": 1558,
"cds_end": null,
"cds_length": 4275,
"cdna_start": 1600,
"cdna_end": null,
"cdna_length": 5464,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"hgvs_c": "c.1558G>A",
"hgvs_p": "p.Asp520Asn",
"transcript": "ENST00000696287.1",
"protein_id": "ENSP00000512524.1",
"transcript_support_level": null,
"aa_start": 520,
"aa_end": null,
"aa_length": 1420,
"cds_start": 1558,
"cds_end": null,
"cds_length": 4263,
"cdna_start": 1601,
"cdna_end": null,
"cdna_length": 4557,
"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": 16,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"hgvs_c": "n.1558G>A",
"hgvs_p": null,
"transcript": "ENST00000561667.2",
"protein_id": "ENSP00000512522.1",
"transcript_support_level": 4,
"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": 6113,
"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": 16,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"hgvs_c": "n.1601G>A",
"hgvs_p": null,
"transcript": "ENST00000567284.7",
"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": 2499,
"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": 10,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"hgvs_c": "n.1519G>A",
"hgvs_p": null,
"transcript": "ENST00000696274.1",
"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": 4600,
"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": 17,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"hgvs_c": "n.*793G>A",
"hgvs_p": null,
"transcript": "ENST00000696275.1",
"protein_id": "ENSP00000512517.1",
"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": 4815,
"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": 16,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"hgvs_c": "n.1601G>A",
"hgvs_p": null,
"transcript": "ENST00000696276.1",
"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": 3025,
"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": 16,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"hgvs_c": "n.1558G>A",
"hgvs_p": null,
"transcript": "ENST00000696286.1",
"protein_id": "ENSP00000512523.1",
"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": 4422,
"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": 15,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"hgvs_c": "n.*902G>A",
"hgvs_p": null,
"transcript": "ENST00000696291.1",
"protein_id": "ENSP00000512530.1",
"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": 4969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"hgvs_c": "n.*793G>A",
"hgvs_p": null,
"transcript": "ENST00000696275.1",
"protein_id": "ENSP00000512517.1",
"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": 4815,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"hgvs_c": "n.*902G>A",
"hgvs_p": null,
"transcript": "ENST00000696291.1",
"protein_id": "ENSP00000512530.1",
"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": 4969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"hgvs_c": "n.*199G>A",
"hgvs_p": null,
"transcript": "ENST00000696277.1",
"protein_id": "ENSP00000512518.1",
"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": 1596,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FANCA",
"gene_hgnc_id": 3582,
"dbsnp": "rs754123446",
"frequency_reference_population": 0.000006196616,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000615742,
"gnomad_genomes_af": 0.00000657324,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.79164719581604,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.635,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7608,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.14,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.223,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000135.4",
"gene_symbol": "FANCA",
"hgnc_id": 3582,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1558G>A",
"hgvs_p": "p.Asp520Asn"
}
],
"clinvar_disease": "Fanconi anemia,Fanconi anemia complementation group A",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Fanconi anemia|Fanconi anemia complementation group A",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}