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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: 11-22625820-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=22625820&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 22625820,
"ref": "G",
"alt": "A",
"effect": "5_prime_UTR_premature_start_codon_gain_variant",
"transcript": "ENST00000327470.6",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCF",
"gene_hgnc_id": 3587,
"hgvs_c": "c.-10C>T",
"hgvs_p": null,
"transcript": "NM_022725.4",
"protein_id": "NP_073562.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 374,
"cds_start": -4,
"cds_end": null,
"cds_length": 1125,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3291,
"mane_select": "ENST00000327470.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCF",
"gene_hgnc_id": 3587,
"hgvs_c": "c.-10C>T",
"hgvs_p": null,
"transcript": "ENST00000327470.6",
"protein_id": "ENSP00000330875.3",
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": 374,
"cds_start": -4,
"cds_end": null,
"cds_length": 1125,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3291,
"mane_select": "NM_022725.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCF",
"gene_hgnc_id": 3587,
"hgvs_c": "c.-10C>T",
"hgvs_p": null,
"transcript": "NM_022725.4",
"protein_id": "NP_073562.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 374,
"cds_start": -4,
"cds_end": null,
"cds_length": 1125,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3291,
"mane_select": "ENST00000327470.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FANCF",
"gene_hgnc_id": 3587,
"hgvs_c": "c.-10C>T",
"hgvs_p": null,
"transcript": "ENST00000327470.6",
"protein_id": "ENSP00000330875.3",
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": 374,
"cds_start": -4,
"cds_end": null,
"cds_length": 1125,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3291,
"mane_select": "NM_022725.4",
"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": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAS2",
"gene_hgnc_id": 4167,
"hgvs_c": "n.312G>A",
"hgvs_p": null,
"transcript": "ENST00000648096.1",
"protein_id": null,
"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": 895,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GAS2",
"gene_hgnc_id": 4167,
"hgvs_c": "c.-21+7G>A",
"hgvs_p": null,
"transcript": "ENST00000528582.5",
"protein_id": "ENSP00000432584.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 180,
"cds_start": -4,
"cds_end": null,
"cds_length": 544,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 736,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAS2",
"gene_hgnc_id": 4167,
"hgvs_c": "c.-2594G>A",
"hgvs_p": null,
"transcript": "XM_011519972.4",
"protein_id": "XP_011518274.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 331,
"cds_start": -4,
"cds_end": null,
"cds_length": 996,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4447,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAS2",
"gene_hgnc_id": 4167,
"hgvs_c": "c.-8625G>A",
"hgvs_p": null,
"transcript": "XM_047426745.1",
"protein_id": "XP_047282701.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 331,
"cds_start": -4,
"cds_end": null,
"cds_length": 996,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10478,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAS2",
"gene_hgnc_id": 4167,
"hgvs_c": "c.-2594G>A",
"hgvs_p": null,
"transcript": "XM_047426746.1",
"protein_id": "XP_047282702.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 313,
"cds_start": -4,
"cds_end": null,
"cds_length": 942,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4393,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FANCF",
"gene_hgnc_id": 3587,
"dbsnp": "rs3740615",
"frequency_reference_population": 0.17387116,
"hom_count_reference_population": 26539,
"allele_count_reference_population": 280530,
"gnomad_exomes_af": 0.176521,
"gnomad_genomes_af": 0.148418,
"gnomad_exomes_ac": 257950,
"gnomad_genomes_ac": 22580,
"gnomad_exomes_homalt": 24481,
"gnomad_genomes_homalt": 2058,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.75,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.75,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -4.165,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000327470.6",
"gene_symbol": "FANCF",
"hgnc_id": 3587,
"effects": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-10C>T",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000528582.5",
"gene_symbol": "GAS2",
"hgnc_id": 4167,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.-21+7G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Fanconi anemia,Fanconi anemia complementation group F,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:8",
"phenotype_combined": "not specified|not provided|Fanconi anemia|Fanconi anemia complementation group F",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}