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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: 3-46439467-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=46439467&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 46439467,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000231751.9",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTF",
"gene_hgnc_id": 6720,
"hgvs_c": "c.1737G>T",
"hgvs_p": "p.Glu579Asp",
"transcript": "NM_002343.6",
"protein_id": "NP_002334.2",
"transcript_support_level": null,
"aa_start": 579,
"aa_end": null,
"aa_length": 710,
"cds_start": 1737,
"cds_end": null,
"cds_length": 2133,
"cdna_start": 1775,
"cdna_end": null,
"cdna_length": 2721,
"mane_select": "ENST00000231751.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTF",
"gene_hgnc_id": 6720,
"hgvs_c": "c.1737G>T",
"hgvs_p": "p.Glu579Asp",
"transcript": "ENST00000231751.9",
"protein_id": "ENSP00000231751.4",
"transcript_support_level": 1,
"aa_start": 579,
"aa_end": null,
"aa_length": 710,
"cds_start": 1737,
"cds_end": null,
"cds_length": 2133,
"cdna_start": 1775,
"cdna_end": null,
"cdna_length": 2721,
"mane_select": "NM_002343.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTF",
"gene_hgnc_id": 6720,
"hgvs_c": "c.1731G>T",
"hgvs_p": "p.Glu577Asp",
"transcript": "ENST00000417439.5",
"protein_id": "ENSP00000405546.1",
"transcript_support_level": 1,
"aa_start": 577,
"aa_end": null,
"aa_length": 708,
"cds_start": 1731,
"cds_end": null,
"cds_length": 2127,
"cdna_start": 1732,
"cdna_end": null,
"cdna_length": 2130,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTF",
"gene_hgnc_id": 6720,
"hgvs_c": "c.1731G>T",
"hgvs_p": "p.Glu577Asp",
"transcript": "NM_001321121.2",
"protein_id": "NP_001308050.1",
"transcript_support_level": null,
"aa_start": 577,
"aa_end": null,
"aa_length": 708,
"cds_start": 1731,
"cds_end": null,
"cds_length": 2127,
"cdna_start": 1769,
"cdna_end": null,
"cdna_length": 2715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTF",
"gene_hgnc_id": 6720,
"hgvs_c": "c.1698G>T",
"hgvs_p": "p.Glu566Asp",
"transcript": "NM_001321122.2",
"protein_id": "NP_001308051.1",
"transcript_support_level": null,
"aa_start": 566,
"aa_end": null,
"aa_length": 697,
"cds_start": 1698,
"cds_end": null,
"cds_length": 2094,
"cdna_start": 2266,
"cdna_end": null,
"cdna_length": 3212,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTF",
"gene_hgnc_id": 6720,
"hgvs_c": "c.1698G>T",
"hgvs_p": "p.Glu566Asp",
"transcript": "ENST00000443496.5",
"protein_id": "ENSP00000397427.1",
"transcript_support_level": 2,
"aa_start": 566,
"aa_end": null,
"aa_length": 695,
"cds_start": 1698,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 2266,
"cdna_end": null,
"cdna_length": 2656,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTF",
"gene_hgnc_id": 6720,
"hgvs_c": "c.1605G>T",
"hgvs_p": "p.Glu535Asp",
"transcript": "NM_001199149.2",
"protein_id": "NP_001186078.1",
"transcript_support_level": null,
"aa_start": 535,
"aa_end": null,
"aa_length": 666,
"cds_start": 1605,
"cds_end": null,
"cds_length": 2001,
"cdna_start": 1905,
"cdna_end": null,
"cdna_length": 2851,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTF",
"gene_hgnc_id": 6720,
"hgvs_c": "c.1605G>T",
"hgvs_p": "p.Glu535Asp",
"transcript": "ENST00000426532.6",
"protein_id": "ENSP00000405719.2",
"transcript_support_level": 2,
"aa_start": 535,
"aa_end": null,
"aa_length": 666,
"cds_start": 1605,
"cds_end": null,
"cds_length": 2001,
"cdna_start": 1922,
"cdna_end": null,
"cdna_length": 2494,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTF",
"gene_hgnc_id": 6720,
"hgvs_c": "n.260G>T",
"hgvs_p": null,
"transcript": "ENST00000478874.2",
"protein_id": null,
"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": 466,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LTF",
"gene_hgnc_id": 6720,
"hgvs_c": "n.226G>T",
"hgvs_p": null,
"transcript": "ENST00000493056.5",
"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": 493,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LTF",
"gene_hgnc_id": 6720,
"dbsnp": "rs2073495",
"frequency_reference_population": 0.00026661728,
"hom_count_reference_population": 5,
"allele_count_reference_population": 429,
"gnomad_exomes_af": 0.000266332,
"gnomad_genomes_af": 0.000269347,
"gnomad_exomes_ac": 388,
"gnomad_genomes_ac": 41,
"gnomad_exomes_homalt": 5,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0049169957637786865,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.015,
"revel_prediction": "Benign",
"alphamissense_score": 0.0973,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.77,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -5.029,
"phylop100way_prediction": "Benign",
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000231751.9",
"gene_symbol": "LTF",
"hgnc_id": 6720,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1737G>T",
"hgvs_p": "p.Glu579Asp"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}