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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: 4-57040828-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=57040828&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 57040828,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001553.3",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFBP7",
"gene_hgnc_id": 5476,
"hgvs_c": "c.581A>G",
"hgvs_p": "p.Asn194Ser",
"transcript": "NM_001553.3",
"protein_id": "NP_001544.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 282,
"cds_start": 581,
"cds_end": null,
"cds_length": 849,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000295666.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001553.3"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFBP7",
"gene_hgnc_id": 5476,
"hgvs_c": "c.581A>G",
"hgvs_p": "p.Asn194Ser",
"transcript": "ENST00000295666.6",
"protein_id": "ENSP00000295666.4",
"transcript_support_level": 1,
"aa_start": 194,
"aa_end": null,
"aa_length": 282,
"cds_start": 581,
"cds_end": null,
"cds_length": 849,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001553.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000295666.6"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFBP7",
"gene_hgnc_id": 5476,
"hgvs_c": "c.689A>G",
"hgvs_p": "p.Asn230Ser",
"transcript": "ENST00000896424.1",
"protein_id": "ENSP00000566483.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 318,
"cds_start": 689,
"cds_end": null,
"cds_length": 957,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896424.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFBP7",
"gene_hgnc_id": 5476,
"hgvs_c": "c.656A>G",
"hgvs_p": "p.Asn219Ser",
"transcript": "ENST00000947223.1",
"protein_id": "ENSP00000617282.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 307,
"cds_start": 656,
"cds_end": null,
"cds_length": 924,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947223.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFBP7",
"gene_hgnc_id": 5476,
"hgvs_c": "c.614A>G",
"hgvs_p": "p.Asn205Ser",
"transcript": "ENST00000896421.1",
"protein_id": "ENSP00000566480.1",
"transcript_support_level": null,
"aa_start": 205,
"aa_end": null,
"aa_length": 293,
"cds_start": 614,
"cds_end": null,
"cds_length": 882,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896421.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFBP7",
"gene_hgnc_id": 5476,
"hgvs_c": "c.611A>G",
"hgvs_p": "p.Asn204Ser",
"transcript": "ENST00000896425.1",
"protein_id": "ENSP00000566484.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 292,
"cds_start": 611,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896425.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFBP7",
"gene_hgnc_id": 5476,
"hgvs_c": "c.581A>G",
"hgvs_p": "p.Asn194Ser",
"transcript": "ENST00000896426.1",
"protein_id": "ENSP00000566485.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 288,
"cds_start": 581,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896426.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFBP7",
"gene_hgnc_id": 5476,
"hgvs_c": "c.581A>G",
"hgvs_p": "p.Asn194Ser",
"transcript": "ENST00000896420.1",
"protein_id": "ENSP00000566479.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 280,
"cds_start": 581,
"cds_end": null,
"cds_length": 843,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896420.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFBP7",
"gene_hgnc_id": 5476,
"hgvs_c": "c.581A>G",
"hgvs_p": "p.Asn194Ser",
"transcript": "NM_001253835.2",
"protein_id": "NP_001240764.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 279,
"cds_start": 581,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001253835.2"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFBP7",
"gene_hgnc_id": 5476,
"hgvs_c": "c.581A>G",
"hgvs_p": "p.Asn194Ser",
"transcript": "ENST00000514062.2",
"protein_id": "ENSP00000486293.1",
"transcript_support_level": 2,
"aa_start": 194,
"aa_end": null,
"aa_length": 279,
"cds_start": 581,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000514062.2"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFBP7",
"gene_hgnc_id": 5476,
"hgvs_c": "c.503A>G",
"hgvs_p": "p.Asn168Ser",
"transcript": "ENST00000896422.1",
"protein_id": "ENSP00000566481.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 256,
"cds_start": 503,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896422.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFBP7",
"gene_hgnc_id": 5476,
"hgvs_c": "c.581A>G",
"hgvs_p": "p.Asn194Ser",
"transcript": "ENST00000896423.1",
"protein_id": "ENSP00000566482.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 243,
"cds_start": 581,
"cds_end": null,
"cds_length": 732,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896423.1"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "IGFBP7",
"gene_hgnc_id": 5476,
"hgvs_c": "c.451-7517A>G",
"hgvs_p": null,
"transcript": "ENST00000896419.1",
"protein_id": "ENSP00000566478.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 237,
"cds_start": null,
"cds_end": null,
"cds_length": 714,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000896419.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGFBP7",
"gene_hgnc_id": 5476,
"hgvs_c": "n.221A>G",
"hgvs_p": null,
"transcript": "ENST00000512512.3",
"protein_id": null,
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000512512.3"
}
],
"gene_symbol": "IGFBP7",
"gene_hgnc_id": 5476,
"dbsnp": "rs200702885",
"frequency_reference_population": 0.000011829839,
"hom_count_reference_population": 0,
"allele_count_reference_population": 19,
"gnomad_exomes_af": 0.0000103181,
"gnomad_genomes_af": 0.0000262553,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2927215099334717,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.087,
"revel_prediction": "Benign",
"alphamissense_score": 0.3402,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.48,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.697,
"phylop100way_prediction": "Uncertain_significance",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001553.3",
"gene_symbol": "IGFBP7",
"hgnc_id": 5476,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.581A>G",
"hgvs_p": "p.Asn194Ser"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}