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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: 12-6870354-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=6870354&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 6870354,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000365.6",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"hgvs_c": "c.721T>C",
"hgvs_p": "p.Phe241Leu",
"transcript": "NM_000365.6",
"protein_id": "NP_000356.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 249,
"cds_start": 721,
"cds_end": null,
"cds_length": 750,
"cdna_start": 757,
"cdna_end": null,
"cdna_length": 1351,
"mane_select": "ENST00000396705.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"hgvs_c": "c.721T>C",
"hgvs_p": "p.Phe241Leu",
"transcript": "ENST00000396705.10",
"protein_id": "ENSP00000379933.4",
"transcript_support_level": 1,
"aa_start": 241,
"aa_end": null,
"aa_length": 249,
"cds_start": 721,
"cds_end": null,
"cds_length": 750,
"cdna_start": 757,
"cdna_end": null,
"cdna_length": 1351,
"mane_select": "NM_000365.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"hgvs_c": "c.832T>C",
"hgvs_p": "p.Phe278Leu",
"transcript": "ENST00000229270.8",
"protein_id": "ENSP00000229270.4",
"transcript_support_level": 1,
"aa_start": 278,
"aa_end": null,
"aa_length": 286,
"cds_start": 832,
"cds_end": null,
"cds_length": 861,
"cdna_start": 1169,
"cdna_end": null,
"cdna_length": 1763,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"hgvs_c": "c.832T>C",
"hgvs_p": "p.Phe278Leu",
"transcript": "ENST00000613953.4",
"protein_id": "ENSP00000484435.1",
"transcript_support_level": 1,
"aa_start": 278,
"aa_end": null,
"aa_length": 286,
"cds_start": 832,
"cds_end": null,
"cds_length": 861,
"cdna_start": 868,
"cdna_end": null,
"cdna_length": 1460,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"hgvs_c": "n.210T>C",
"hgvs_p": null,
"transcript": "ENST00000474253.1",
"protein_id": null,
"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": 427,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"hgvs_c": "c.832T>C",
"hgvs_p": "p.Phe278Leu",
"transcript": "NM_001159287.1",
"protein_id": "NP_001152759.1",
"transcript_support_level": null,
"aa_start": 278,
"aa_end": null,
"aa_length": 286,
"cds_start": 832,
"cds_end": null,
"cds_length": 861,
"cdna_start": 868,
"cdna_end": null,
"cdna_length": 1460,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"hgvs_c": "c.475T>C",
"hgvs_p": "p.Phe159Leu",
"transcript": "NM_001258026.2",
"protein_id": "NP_001244955.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 167,
"cds_start": 475,
"cds_end": null,
"cds_length": 504,
"cdna_start": 1011,
"cdna_end": null,
"cdna_length": 1605,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"hgvs_c": "c.475T>C",
"hgvs_p": "p.Phe159Leu",
"transcript": "ENST00000488464.6",
"protein_id": "ENSP00000475620.1",
"transcript_support_level": 5,
"aa_start": 159,
"aa_end": null,
"aa_length": 167,
"cds_start": 475,
"cds_end": null,
"cds_length": 504,
"cdna_start": 762,
"cdna_end": null,
"cdna_length": 791,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"hgvs_c": "c.475T>C",
"hgvs_p": "p.Phe159Leu",
"transcript": "ENST00000535434.5",
"protein_id": "ENSP00000443599.1",
"transcript_support_level": 2,
"aa_start": 159,
"aa_end": null,
"aa_length": 167,
"cds_start": 475,
"cds_end": null,
"cds_length": 504,
"cdna_start": 1002,
"cdna_end": null,
"cdna_length": 1587,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"hgvs_c": "n.*217T>C",
"hgvs_p": null,
"transcript": "ENST00000482209.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 328,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TPI1",
"gene_hgnc_id": 12009,
"dbsnp": "rs121964847",
"frequency_reference_population": 0.0000013682624,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136826,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.983739972114563,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.911,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9972,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.59,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.983,
"phylop100way_prediction": "Pathogenic",
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Strong",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "NM_000365.6",
"gene_symbol": "TPI1",
"hgnc_id": 12009,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.721T>C",
"hgvs_p": "p.Phe241Leu"
}
],
"clinvar_disease": "Triosephosphate isomerase deficiency",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Triosephosphate isomerase deficiency",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}