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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: 1-1041249-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=1041249&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 1041249,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000379370.7",
"consequences": [
{
"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": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGRN",
"gene_hgnc_id": 329,
"hgvs_c": "c.804C>T",
"hgvs_p": "p.Ala268Ala",
"transcript": "NM_198576.4",
"protein_id": "NP_940978.2",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 2045,
"cds_start": 804,
"cds_end": null,
"cds_length": 6138,
"cdna_start": 857,
"cdna_end": null,
"cdna_length": 7326,
"mane_select": "ENST00000379370.7",
"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": 5,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGRN",
"gene_hgnc_id": 329,
"hgvs_c": "c.804C>T",
"hgvs_p": "p.Ala268Ala",
"transcript": "ENST00000379370.7",
"protein_id": "ENSP00000368678.2",
"transcript_support_level": 1,
"aa_start": 268,
"aa_end": null,
"aa_length": 2045,
"cds_start": 804,
"cds_end": null,
"cds_length": 6138,
"cdna_start": 857,
"cdna_end": null,
"cdna_length": 7326,
"mane_select": "NM_198576.4",
"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": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGRN",
"gene_hgnc_id": 329,
"hgvs_c": "c.804C>T",
"hgvs_p": "p.Ala268Ala",
"transcript": "NM_001305275.2",
"protein_id": "NP_001292204.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 2068,
"cds_start": 804,
"cds_end": null,
"cds_length": 6207,
"cdna_start": 857,
"cdna_end": null,
"cdna_length": 7395,
"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": 4,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGRN",
"gene_hgnc_id": 329,
"hgvs_c": "c.489C>T",
"hgvs_p": "p.Ala163Ala",
"transcript": "ENST00000651234.1",
"protein_id": "ENSP00000499046.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 1963,
"cds_start": 489,
"cds_end": null,
"cds_length": 5892,
"cdna_start": 939,
"cdna_end": null,
"cdna_length": 7477,
"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": 4,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGRN",
"gene_hgnc_id": 329,
"hgvs_c": "c.489C>T",
"hgvs_p": "p.Ala163Ala",
"transcript": "NM_001364727.2",
"protein_id": "NP_001351656.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 1944,
"cds_start": 489,
"cds_end": null,
"cds_length": 5835,
"cdna_start": 1052,
"cdna_end": null,
"cdna_length": 7533,
"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": 4,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGRN",
"gene_hgnc_id": 329,
"hgvs_c": "c.489C>T",
"hgvs_p": "p.Ala163Ala",
"transcript": "ENST00000652369.2",
"protein_id": "ENSP00000498543.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 1940,
"cds_start": 489,
"cds_end": null,
"cds_length": 5823,
"cdna_start": 939,
"cdna_end": null,
"cdna_length": 7411,
"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": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGRN",
"gene_hgnc_id": 329,
"hgvs_c": "c.390C>T",
"hgvs_p": "p.Ala130Ala",
"transcript": "ENST00000620552.4",
"protein_id": "ENSP00000484607.1",
"transcript_support_level": 5,
"aa_start": 130,
"aa_end": null,
"aa_length": 1930,
"cds_start": 390,
"cds_end": null,
"cds_length": 5793,
"cdna_start": 854,
"cdna_end": null,
"cdna_length": 7394,
"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": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGRN",
"gene_hgnc_id": 329,
"hgvs_c": "c.804C>T",
"hgvs_p": "p.Ala268Ala",
"transcript": "XM_005244749.4",
"protein_id": "XP_005244806.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 2049,
"cds_start": 804,
"cds_end": null,
"cds_length": 6150,
"cdna_start": 857,
"cdna_end": null,
"cdna_length": 7338,
"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": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGRN",
"gene_hgnc_id": 329,
"hgvs_c": "c.804C>T",
"hgvs_p": "p.Ala268Ala",
"transcript": "XM_011541429.3",
"protein_id": "XP_011539731.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 2004,
"cds_start": 804,
"cds_end": null,
"cds_length": 6015,
"cdna_start": 857,
"cdna_end": null,
"cdna_length": 6785,
"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": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGRN",
"gene_hgnc_id": 329,
"hgvs_c": "c.804C>T",
"hgvs_p": "p.Ala268Ala",
"transcript": "XM_047419836.1",
"protein_id": "XP_047275792.1",
"transcript_support_level": null,
"aa_start": 268,
"aa_end": null,
"aa_length": 2000,
"cds_start": 804,
"cds_end": null,
"cds_length": 6003,
"cdna_start": 857,
"cdna_end": null,
"cdna_length": 6773,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGRN",
"gene_hgnc_id": 329,
"hgvs_c": "n.751C>T",
"hgvs_p": null,
"transcript": "ENST00000469403.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AGRN",
"gene_hgnc_id": 329,
"dbsnp": "rs113789806",
"frequency_reference_population": 0.008446099,
"hom_count_reference_population": 746,
"allele_count_reference_population": 12638,
"gnomad_exomes_af": 0.00455666,
"gnomad_genomes_af": 0.0428686,
"gnomad_exomes_ac": 6126,
"gnomad_genomes_ac": 6512,
"gnomad_exomes_homalt": 336,
"gnomad_genomes_homalt": 410,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.49000000953674316,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.048,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000379370.7",
"gene_symbol": "AGRN",
"hgnc_id": 329,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.804C>T",
"hgvs_p": "p.Ala268Ala"
}
],
"clinvar_disease": "Congenital myasthenic syndrome 8,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "not specified|Congenital myasthenic syndrome 8|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}