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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: 8-60865138-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=60865138&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 60865138,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_017780.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "c.8199T>C",
"hgvs_p": "p.Ala2733Ala",
"transcript": "NM_017780.4",
"protein_id": "NP_060250.2",
"transcript_support_level": null,
"aa_start": 2733,
"aa_end": null,
"aa_length": 2997,
"cds_start": 8199,
"cds_end": null,
"cds_length": 8994,
"cdna_start": 8716,
"cdna_end": null,
"cdna_length": 11606,
"mane_select": "ENST00000423902.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "c.8199T>C",
"hgvs_p": "p.Ala2733Ala",
"transcript": "ENST00000423902.7",
"protein_id": "ENSP00000392028.1",
"transcript_support_level": 5,
"aa_start": 2733,
"aa_end": null,
"aa_length": 2997,
"cds_start": 8199,
"cds_end": null,
"cds_length": 8994,
"cdna_start": 8716,
"cdna_end": null,
"cdna_length": 11606,
"mane_select": "NM_017780.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "c.2052T>C",
"hgvs_p": "p.Ala684Ala",
"transcript": "ENST00000524602.5",
"protein_id": "ENSP00000437061.1",
"transcript_support_level": 1,
"aa_start": 684,
"aa_end": null,
"aa_length": 948,
"cds_start": 2052,
"cds_end": null,
"cds_length": 2847,
"cdna_start": 2120,
"cdna_end": null,
"cdna_length": 3456,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "c.2052T>C",
"hgvs_p": "p.Ala684Ala",
"transcript": "NM_001316690.1",
"protein_id": "NP_001303619.1",
"transcript_support_level": null,
"aa_start": 684,
"aa_end": null,
"aa_length": 948,
"cds_start": 2052,
"cds_end": null,
"cds_length": 2847,
"cdna_start": 2226,
"cdna_end": null,
"cdna_length": 5116,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "c.8289T>C",
"hgvs_p": "p.Ala2763Ala",
"transcript": "XM_011517553.3",
"protein_id": "XP_011515855.1",
"transcript_support_level": null,
"aa_start": 2763,
"aa_end": null,
"aa_length": 3027,
"cds_start": 8289,
"cds_end": null,
"cds_length": 9084,
"cdna_start": 8806,
"cdna_end": null,
"cdna_length": 11696,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "c.8289T>C",
"hgvs_p": "p.Ala2763Ala",
"transcript": "XM_011517554.4",
"protein_id": "XP_011515856.1",
"transcript_support_level": null,
"aa_start": 2763,
"aa_end": null,
"aa_length": 3027,
"cds_start": 8289,
"cds_end": null,
"cds_length": 9084,
"cdna_start": 8760,
"cdna_end": null,
"cdna_length": 11650,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "c.8289T>C",
"hgvs_p": "p.Ala2763Ala",
"transcript": "XM_017013612.2",
"protein_id": "XP_016869101.1",
"transcript_support_level": null,
"aa_start": 2763,
"aa_end": null,
"aa_length": 3027,
"cds_start": 8289,
"cds_end": null,
"cds_length": 9084,
"cdna_start": 8821,
"cdna_end": null,
"cdna_length": 11711,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "c.8286T>C",
"hgvs_p": "p.Ala2762Ala",
"transcript": "XM_011517555.3",
"protein_id": "XP_011515857.1",
"transcript_support_level": null,
"aa_start": 2762,
"aa_end": null,
"aa_length": 3026,
"cds_start": 8286,
"cds_end": null,
"cds_length": 9081,
"cdna_start": 8803,
"cdna_end": null,
"cdna_length": 11693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "c.8196T>C",
"hgvs_p": "p.Ala2732Ala",
"transcript": "XM_017013613.2",
"protein_id": "XP_016869102.1",
"transcript_support_level": null,
"aa_start": 2732,
"aa_end": null,
"aa_length": 2996,
"cds_start": 8196,
"cds_end": null,
"cds_length": 8991,
"cdna_start": 8713,
"cdna_end": null,
"cdna_length": 11603,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "c.8067T>C",
"hgvs_p": "p.Ala2689Ala",
"transcript": "XM_047421945.1",
"protein_id": "XP_047277901.1",
"transcript_support_level": null,
"aa_start": 2689,
"aa_end": null,
"aa_length": 2953,
"cds_start": 8067,
"cds_end": null,
"cds_length": 8862,
"cdna_start": 8584,
"cdna_end": null,
"cdna_length": 11474,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "c.8064T>C",
"hgvs_p": "p.Ala2688Ala",
"transcript": "XM_047421946.1",
"protein_id": "XP_047277902.1",
"transcript_support_level": null,
"aa_start": 2688,
"aa_end": null,
"aa_length": 2952,
"cds_start": 8064,
"cds_end": null,
"cds_length": 8859,
"cdna_start": 8581,
"cdna_end": null,
"cdna_length": 11471,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "c.7974T>C",
"hgvs_p": "p.Ala2658Ala",
"transcript": "XM_047421947.1",
"protein_id": "XP_047277903.1",
"transcript_support_level": null,
"aa_start": 2658,
"aa_end": null,
"aa_length": 2922,
"cds_start": 7974,
"cds_end": null,
"cds_length": 8769,
"cdna_start": 8491,
"cdna_end": null,
"cdna_length": 11381,
"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": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "n.245T>C",
"hgvs_p": null,
"transcript": "ENST00000528280.1",
"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": 566,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "n.1375T>C",
"hgvs_p": null,
"transcript": "ENST00000695850.1",
"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": 3726,
"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": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "n.306T>C",
"hgvs_p": null,
"transcript": "ENST00000695852.1",
"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": 2054,
"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": 37,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "n.*1258T>C",
"hgvs_p": null,
"transcript": "ENST00000695853.1",
"protein_id": "ENSP00000512218.1",
"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": 10902,
"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": 37,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "n.*1258T>C",
"hgvs_p": null,
"transcript": "ENST00000695853.1",
"protein_id": "ENSP00000512218.1",
"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": 10902,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "n.*5T>C",
"hgvs_p": null,
"transcript": "ENST00000532149.1",
"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": 616,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"hgvs_c": "n.*13T>C",
"hgvs_p": null,
"transcript": "ENST00000618450.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 4222,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CHD7",
"gene_hgnc_id": 20626,
"dbsnp": "rs878855033",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7099999785423279,
"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": -0.71,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -5.083,
"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": "NM_017780.4",
"gene_symbol": "CHD7",
"hgnc_id": 20626,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.8199T>C",
"hgvs_p": "p.Ala2733Ala"
}
],
"clinvar_disease": "CHARGE syndrome",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "CHARGE syndrome",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}