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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: 9-69064942-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=69064942&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 69064942,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000484259.3",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FXN",
"gene_hgnc_id": 3951,
"hgvs_c": "c.389G>T",
"hgvs_p": "p.Gly130Val",
"transcript": "NM_000144.5",
"protein_id": "NP_000135.2",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 210,
"cds_start": 389,
"cds_end": null,
"cds_length": 633,
"cdna_start": 420,
"cdna_end": null,
"cdna_length": 6978,
"mane_select": "ENST00000484259.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FXN",
"gene_hgnc_id": 3951,
"hgvs_c": "c.389G>T",
"hgvs_p": "p.Gly130Val",
"transcript": "ENST00000484259.3",
"protein_id": "ENSP00000419243.2",
"transcript_support_level": 3,
"aa_start": 130,
"aa_end": null,
"aa_length": 210,
"cds_start": 389,
"cds_end": null,
"cds_length": 633,
"cdna_start": 420,
"cdna_end": null,
"cdna_length": 6978,
"mane_select": "NM_000144.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FXN",
"gene_hgnc_id": 3951,
"hgvs_c": "c.164G>T",
"hgvs_p": "p.Gly55Val",
"transcript": "ENST00000377270.8",
"protein_id": "ENSP00000366482.4",
"transcript_support_level": 1,
"aa_start": 55,
"aa_end": null,
"aa_length": 135,
"cds_start": 164,
"cds_end": null,
"cds_length": 408,
"cdna_start": 480,
"cdna_end": null,
"cdna_length": 2843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FXN",
"gene_hgnc_id": 3951,
"hgvs_c": "c.164G>T",
"hgvs_p": "p.Gly55Val",
"transcript": "ENST00000498653.5",
"protein_id": "ENSP00000418015.1",
"transcript_support_level": 1,
"aa_start": 55,
"aa_end": null,
"aa_length": 135,
"cds_start": 164,
"cds_end": null,
"cds_length": 408,
"cdna_start": 269,
"cdna_end": null,
"cdna_length": 856,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285130",
"gene_hgnc_id": null,
"hgvs_c": "c.165+28995G>T",
"hgvs_p": null,
"transcript": "ENST00000642889.1",
"protein_id": "ENSP00000493780.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1319,
"cds_start": -4,
"cds_end": null,
"cds_length": 3960,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4806,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FXN",
"gene_hgnc_id": 3951,
"hgvs_c": "c.389G>T",
"hgvs_p": "p.Gly130Val",
"transcript": "NM_181425.3",
"protein_id": "NP_852090.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 196,
"cds_start": 389,
"cds_end": null,
"cds_length": 591,
"cdna_start": 420,
"cdna_end": null,
"cdna_length": 6986,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FXN",
"gene_hgnc_id": 3951,
"hgvs_c": "c.389G>T",
"hgvs_p": "p.Gly130Val",
"transcript": "ENST00000396366.6",
"protein_id": "ENSP00000379652.2",
"transcript_support_level": 2,
"aa_start": 130,
"aa_end": null,
"aa_length": 196,
"cds_start": 389,
"cds_end": null,
"cds_length": 591,
"cdna_start": 410,
"cdna_end": null,
"cdna_length": 922,
"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": 4,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285130",
"gene_hgnc_id": null,
"hgvs_c": "n.389G>T",
"hgvs_p": null,
"transcript": "ENST00000643352.1",
"protein_id": "ENSP00000496488.1",
"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": 4322,
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285130",
"gene_hgnc_id": null,
"hgvs_c": "n.386G>T",
"hgvs_p": null,
"transcript": "ENST00000643765.1",
"protein_id": "ENSP00000494300.1",
"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": 844,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FXN",
"gene_hgnc_id": 3951,
"hgvs_c": "n.268G>T",
"hgvs_p": null,
"transcript": "ENST00000644653.1",
"protein_id": "ENSP00000495217.1",
"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": 2632,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285130",
"gene_hgnc_id": null,
"hgvs_c": "n.*114G>T",
"hgvs_p": null,
"transcript": "ENST00000644977.1",
"protein_id": "ENSP00000495651.1",
"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": 531,
"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": 3,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285130",
"gene_hgnc_id": null,
"hgvs_c": "n.268G>T",
"hgvs_p": null,
"transcript": "ENST00000645088.1",
"protein_id": "ENSP00000495447.1",
"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": 6106,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285130",
"gene_hgnc_id": null,
"hgvs_c": "n.*114G>T",
"hgvs_p": null,
"transcript": "ENST00000644977.1",
"protein_id": "ENSP00000495651.1",
"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": 531,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285130",
"gene_hgnc_id": null,
"hgvs_c": "c.384+11682G>T",
"hgvs_p": null,
"transcript": "ENST00000646862.1",
"protein_id": "ENSP00000494599.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 224,
"cds_start": -4,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 689,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285130",
"gene_hgnc_id": null,
"hgvs_c": "n.384+11682G>T",
"hgvs_p": null,
"transcript": "ENST00000642330.1",
"protein_id": "ENSP00000493770.1",
"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": 2156,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FXN",
"gene_hgnc_id": 3951,
"dbsnp": "rs104894107",
"frequency_reference_population": 0.0000417144,
"hom_count_reference_population": 0,
"allele_count_reference_population": 67,
"gnomad_exomes_af": 0.0000426396,
"gnomad_genomes_af": 0.0000328701,
"gnomad_exomes_ac": 62,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9641710519790649,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.99,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9661,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.61,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.302,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000484259.3",
"gene_symbol": "FXN",
"hgnc_id": 3951,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.389G>T",
"hgvs_p": "p.Gly130Val"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000642889.1",
"gene_symbol": "ENSG00000285130",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.165+28995G>T",
"hgvs_p": null
}
],
"clinvar_disease": "Friedreich ataxia,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:2 LP:1 US:1",
"phenotype_combined": "Friedreich ataxia|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}