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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: 19-6380324-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=6380324&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 6380324,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002096.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTF2F1",
"gene_hgnc_id": 4652,
"hgvs_c": "c.1511G>A",
"hgvs_p": "p.Arg504His",
"transcript": "NM_002096.3",
"protein_id": "NP_002087.2",
"transcript_support_level": null,
"aa_start": 504,
"aa_end": null,
"aa_length": 517,
"cds_start": 1511,
"cds_end": null,
"cds_length": 1554,
"cdna_start": 1680,
"cdna_end": null,
"cdna_length": 2432,
"mane_select": "ENST00000394456.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002096.3"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTF2F1",
"gene_hgnc_id": 4652,
"hgvs_c": "c.1511G>A",
"hgvs_p": "p.Arg504His",
"transcript": "ENST00000394456.10",
"protein_id": "ENSP00000377969.3",
"transcript_support_level": 1,
"aa_start": 504,
"aa_end": null,
"aa_length": 517,
"cds_start": 1511,
"cds_end": null,
"cds_length": 1554,
"cdna_start": 1680,
"cdna_end": null,
"cdna_length": 2432,
"mane_select": "NM_002096.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000394456.10"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTF2F1",
"gene_hgnc_id": 4652,
"hgvs_c": "c.1508G>A",
"hgvs_p": "p.Arg503His",
"transcript": "ENST00000869875.1",
"protein_id": "ENSP00000539934.1",
"transcript_support_level": null,
"aa_start": 503,
"aa_end": null,
"aa_length": 516,
"cds_start": 1508,
"cds_end": null,
"cds_length": 1551,
"cdna_start": 1677,
"cdna_end": null,
"cdna_length": 2406,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000869875.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTF2F1",
"gene_hgnc_id": 4652,
"hgvs_c": "c.1505G>A",
"hgvs_p": "p.Arg502His",
"transcript": "ENST00000933129.1",
"protein_id": "ENSP00000603188.1",
"transcript_support_level": null,
"aa_start": 502,
"aa_end": null,
"aa_length": 515,
"cds_start": 1505,
"cds_end": null,
"cds_length": 1548,
"cdna_start": 1674,
"cdna_end": null,
"cdna_length": 2426,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933129.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTF2F1",
"gene_hgnc_id": 4652,
"hgvs_c": "c.1484G>A",
"hgvs_p": "p.Arg495His",
"transcript": "ENST00000933130.1",
"protein_id": "ENSP00000603189.1",
"transcript_support_level": null,
"aa_start": 495,
"aa_end": null,
"aa_length": 508,
"cds_start": 1484,
"cds_end": null,
"cds_length": 1527,
"cdna_start": 1653,
"cdna_end": null,
"cdna_length": 1802,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933130.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTF2F1",
"gene_hgnc_id": 4652,
"hgvs_c": "c.1259G>A",
"hgvs_p": "p.Arg420His",
"transcript": "ENST00000593678.5",
"protein_id": "ENSP00000469091.1",
"transcript_support_level": 2,
"aa_start": 420,
"aa_end": null,
"aa_length": 433,
"cds_start": 1259,
"cds_end": null,
"cds_length": 1302,
"cdna_start": 1259,
"cdna_end": null,
"cdna_length": 1705,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000593678.5"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTF2F1",
"gene_hgnc_id": 4652,
"hgvs_c": "c.1538G>A",
"hgvs_p": "p.Arg513His",
"transcript": "XM_047438710.1",
"protein_id": "XP_047294666.1",
"transcript_support_level": null,
"aa_start": 513,
"aa_end": null,
"aa_length": 526,
"cds_start": 1538,
"cds_end": null,
"cds_length": 1581,
"cdna_start": 1662,
"cdna_end": null,
"cdna_length": 2414,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438710.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTF2F1",
"gene_hgnc_id": 4652,
"hgvs_c": "n.868G>A",
"hgvs_p": null,
"transcript": "ENST00000594213.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1002,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000594213.5"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTF2F1",
"gene_hgnc_id": 4652,
"hgvs_c": "n.*67G>A",
"hgvs_p": null,
"transcript": "ENST00000594965.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 762,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000594965.1"
}
],
"gene_symbol": "GTF2F1",
"gene_hgnc_id": 4652,
"dbsnp": "rs146571246",
"frequency_reference_population": 0.00009540956,
"hom_count_reference_population": 0,
"allele_count_reference_population": 154,
"gnomad_exomes_af": 0.0000985032,
"gnomad_genomes_af": 0.0000656978,
"gnomad_exomes_ac": 144,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11881855130195618,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.193,
"revel_prediction": "Benign",
"alphamissense_score": 0.817,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.19,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.448,
"phylop100way_prediction": "Uncertain_significance",
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_002096.3",
"gene_symbol": "GTF2F1",
"hgnc_id": 4652,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1511G>A",
"hgvs_p": "p.Arg504His"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}