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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: 7-100620974-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=100620974&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 100620974,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000223051.8",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "c.2289C>T",
"hgvs_p": "p.Ser763Ser",
"transcript": "NM_003227.4",
"protein_id": "NP_003218.2",
"transcript_support_level": null,
"aa_start": 763,
"aa_end": null,
"aa_length": 801,
"cds_start": 2289,
"cds_end": null,
"cds_length": 2406,
"cdna_start": 2332,
"cdna_end": null,
"cdna_length": 2886,
"mane_select": "ENST00000223051.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "c.2289C>T",
"hgvs_p": "p.Ser763Ser",
"transcript": "ENST00000223051.8",
"protein_id": "ENSP00000223051.3",
"transcript_support_level": 1,
"aa_start": 763,
"aa_end": null,
"aa_length": 801,
"cds_start": 2289,
"cds_end": null,
"cds_length": 2406,
"cdna_start": 2332,
"cdna_end": null,
"cdna_length": 2886,
"mane_select": "NM_003227.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "c.2289C>T",
"hgvs_p": "p.Ser763Ser",
"transcript": "ENST00000462107.1",
"protein_id": "ENSP00000420525.1",
"transcript_support_level": 5,
"aa_start": 763,
"aa_end": null,
"aa_length": 801,
"cds_start": 2289,
"cds_end": null,
"cds_length": 2406,
"cdna_start": 2577,
"cdna_end": null,
"cdna_length": 3131,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "c.1776C>T",
"hgvs_p": "p.Ser592Ser",
"transcript": "NM_001206855.3",
"protein_id": "NP_001193784.1",
"transcript_support_level": null,
"aa_start": 592,
"aa_end": null,
"aa_length": 630,
"cds_start": 1776,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1910,
"cdna_end": null,
"cdna_length": 2464,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "n.1325C>T",
"hgvs_p": null,
"transcript": "ENST00000462090.5",
"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": 1844,
"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": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "n.2209C>T",
"hgvs_p": null,
"transcript": "ENST00000465294.5",
"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": 2763,
"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": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "n.1910C>T",
"hgvs_p": null,
"transcript": "ENST00000476304.5",
"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": 2421,
"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": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "n.*1133C>T",
"hgvs_p": null,
"transcript": "ENST00000490084.5",
"protein_id": "ENSP00000418942.1",
"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": 2196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "c.*964C>T",
"hgvs_p": null,
"transcript": "ENST00000431692.5",
"protein_id": "ENSP00000413905.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 355,
"cds_start": -4,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2631,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"hgvs_c": "n.*1133C>T",
"hgvs_p": null,
"transcript": "ENST00000490084.5",
"protein_id": "ENSP00000418942.1",
"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": 2196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TFR2",
"gene_hgnc_id": 11762,
"dbsnp": "rs374915672",
"frequency_reference_population": 0.00004650286,
"hom_count_reference_population": 0,
"allele_count_reference_population": 75,
"gnomad_exomes_af": 0.0000486116,
"gnomad_genomes_af": 0.0000262733,
"gnomad_exomes_ac": 71,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8399999737739563,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.84,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.014,
"phylop100way_prediction": "Benign",
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 7,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000223051.8",
"gene_symbol": "TFR2",
"hgnc_id": 11762,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2289C>T",
"hgvs_p": "p.Ser763Ser"
}
],
"clinvar_disease": "Hereditary hemochromatosis",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Hereditary hemochromatosis",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}