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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: 19-3730507-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=3730507&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 3730507,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_001267561.2",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.414C>T",
"hgvs_p": "p.Ser138Ser",
"transcript": "NM_001267560.2",
"protein_id": "NP_001254489.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 919,
"cds_start": 414,
"cds_end": null,
"cds_length": 2760,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000541714.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001267560.2"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.414C>T",
"hgvs_p": "p.Ser138Ser",
"transcript": "ENST00000541714.7",
"protein_id": "ENSP00000439278.1",
"transcript_support_level": 2,
"aa_start": 138,
"aa_end": null,
"aa_length": 919,
"cds_start": 414,
"cds_end": null,
"cds_length": 2760,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001267560.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000541714.7"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.471C>T",
"hgvs_p": "p.Ser157Ser",
"transcript": "ENST00000587686.1",
"protein_id": "ENSP00000467864.1",
"transcript_support_level": 1,
"aa_start": 157,
"aa_end": null,
"aa_length": 938,
"cds_start": 471,
"cds_end": null,
"cds_length": 2817,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000587686.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.441C>T",
"hgvs_p": "p.Ser147Ser",
"transcript": "NM_001267561.2",
"protein_id": "NP_001254490.1",
"transcript_support_level": null,
"aa_start": 147,
"aa_end": null,
"aa_length": 928,
"cds_start": 441,
"cds_end": null,
"cds_length": 2787,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001267561.2"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.441C>T",
"hgvs_p": "p.Ser147Ser",
"transcript": "ENST00000589378.5",
"protein_id": "ENSP00000465419.1",
"transcript_support_level": 2,
"aa_start": 147,
"aa_end": null,
"aa_length": 928,
"cds_start": 441,
"cds_end": null,
"cds_length": 2787,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000589378.5"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.414C>T",
"hgvs_p": "p.Ser138Ser",
"transcript": "ENST00000872696.1",
"protein_id": "ENSP00000542755.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 919,
"cds_start": 414,
"cds_end": null,
"cds_length": 2760,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872696.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.414C>T",
"hgvs_p": "p.Ser138Ser",
"transcript": "ENST00000872697.1",
"protein_id": "ENSP00000542756.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 919,
"cds_start": 414,
"cds_end": null,
"cds_length": 2760,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872697.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.414C>T",
"hgvs_p": "p.Ser138Ser",
"transcript": "ENST00000872698.1",
"protein_id": "ENSP00000542757.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 919,
"cds_start": 414,
"cds_end": null,
"cds_length": 2760,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872698.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.414C>T",
"hgvs_p": "p.Ser138Ser",
"transcript": "ENST00000872700.1",
"protein_id": "ENSP00000542759.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 919,
"cds_start": 414,
"cds_end": null,
"cds_length": 2760,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872700.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.414C>T",
"hgvs_p": "p.Ser138Ser",
"transcript": "ENST00000872701.1",
"protein_id": "ENSP00000542760.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 919,
"cds_start": 414,
"cds_end": null,
"cds_length": 2760,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872701.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.414C>T",
"hgvs_p": "p.Ser138Ser",
"transcript": "ENST00000956533.1",
"protein_id": "ENSP00000626592.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 919,
"cds_start": 414,
"cds_end": null,
"cds_length": 2760,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956533.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.414C>T",
"hgvs_p": "p.Ser138Ser",
"transcript": "ENST00000956534.1",
"protein_id": "ENSP00000626593.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 919,
"cds_start": 414,
"cds_end": null,
"cds_length": 2760,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956534.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.414C>T",
"hgvs_p": "p.Ser138Ser",
"transcript": "ENST00000956535.1",
"protein_id": "ENSP00000626594.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 919,
"cds_start": 414,
"cds_end": null,
"cds_length": 2760,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956535.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.414C>T",
"hgvs_p": "p.Ser138Ser",
"transcript": "ENST00000956536.1",
"protein_id": "ENSP00000626595.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 919,
"cds_start": 414,
"cds_end": null,
"cds_length": 2760,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956536.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.306C>T",
"hgvs_p": "p.Ser102Ser",
"transcript": "ENST00000539908.6",
"protein_id": "ENSP00000439991.1",
"transcript_support_level": 2,
"aa_start": 102,
"aa_end": null,
"aa_length": 883,
"cds_start": 306,
"cds_end": null,
"cds_length": 2652,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000539908.6"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.414C>T",
"hgvs_p": "p.Ser138Ser",
"transcript": "ENST00000872695.1",
"protein_id": "ENSP00000542754.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 876,
"cds_start": 414,
"cds_end": null,
"cds_length": 2631,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872695.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.414C>T",
"hgvs_p": "p.Ser138Ser",
"transcript": "ENST00000872699.1",
"protein_id": "ENSP00000542758.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 823,
"cds_start": 414,
"cds_end": null,
"cds_length": 2472,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872699.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.414C>T",
"hgvs_p": "p.Ser138Ser",
"transcript": "ENST00000956532.1",
"protein_id": "ENSP00000626591.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 823,
"cds_start": 414,
"cds_end": null,
"cds_length": 2472,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956532.1"
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.612C>T",
"hgvs_p": "p.Ser204Ser",
"transcript": "XM_047438611.1",
"protein_id": "XP_047294567.1",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 985,
"cds_start": 612,
"cds_end": null,
"cds_length": 2958,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047438611.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "c.*73C>T",
"hgvs_p": null,
"transcript": "ENST00000590545.5",
"protein_id": "ENSP00000468641.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 122,
"cds_start": null,
"cds_end": null,
"cds_length": 371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000590545.5"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"hgvs_c": "n.*220C>T",
"hgvs_p": null,
"transcript": "ENST00000587912.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000587912.1"
}
],
"gene_symbol": "TJP3",
"gene_hgnc_id": 11829,
"dbsnp": "rs199667693",
"frequency_reference_population": 0.0004313211,
"hom_count_reference_population": 6,
"allele_count_reference_population": 685,
"gnomad_exomes_af": 0.000429717,
"gnomad_genomes_af": 0.000446446,
"gnomad_exomes_ac": 617,
"gnomad_genomes_ac": 68,
"gnomad_exomes_homalt": 6,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6000000238418579,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.6,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -7.536,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7,BS2",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 11,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001267561.2",
"gene_symbol": "TJP3",
"hgnc_id": 11829,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.441C>T",
"hgvs_p": "p.Ser147Ser"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}