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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: 19-48472392-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=48472392&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 48472392,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004228.7",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYTH2",
"gene_hgnc_id": 9502,
"hgvs_c": "c.302A>T",
"hgvs_p": "p.Tyr101Phe",
"transcript": "NM_004228.7",
"protein_id": "NP_004219.3",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 399,
"cds_start": 302,
"cds_end": null,
"cds_length": 1200,
"cdna_start": 441,
"cdna_end": null,
"cdna_length": 4443,
"mane_select": "ENST00000452733.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYTH2",
"gene_hgnc_id": 9502,
"hgvs_c": "c.302A>T",
"hgvs_p": "p.Tyr101Phe",
"transcript": "ENST00000452733.7",
"protein_id": "ENSP00000408236.2",
"transcript_support_level": 1,
"aa_start": 101,
"aa_end": null,
"aa_length": 399,
"cds_start": 302,
"cds_end": null,
"cds_length": 1200,
"cdna_start": 441,
"cdna_end": null,
"cdna_length": 4443,
"mane_select": "NM_004228.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYTH2",
"gene_hgnc_id": 9502,
"hgvs_c": "c.302A>T",
"hgvs_p": "p.Tyr101Phe",
"transcript": "ENST00000427476.4",
"protein_id": "ENSP00000486578.1",
"transcript_support_level": 1,
"aa_start": 101,
"aa_end": null,
"aa_length": 400,
"cds_start": 302,
"cds_end": null,
"cds_length": 1203,
"cdna_start": 602,
"cdna_end": null,
"cdna_length": 4606,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000268465",
"gene_hgnc_id": null,
"hgvs_c": "c.254A>T",
"hgvs_p": "p.Tyr85Phe",
"transcript": "ENST00000595676.1",
"protein_id": "ENSP00000470383.1",
"transcript_support_level": 2,
"aa_start": 85,
"aa_end": null,
"aa_length": 96,
"cds_start": 254,
"cds_end": null,
"cds_length": 293,
"cdna_start": 404,
"cdna_end": null,
"cdna_length": 443,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYTH2",
"gene_hgnc_id": 9502,
"hgvs_c": "c.437A>T",
"hgvs_p": "p.Tyr146Phe",
"transcript": "ENST00000704950.1",
"protein_id": "ENSP00000516062.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 444,
"cds_start": 437,
"cds_end": null,
"cds_length": 1335,
"cdna_start": 441,
"cdna_end": null,
"cdna_length": 4443,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYTH2",
"gene_hgnc_id": 9502,
"hgvs_c": "c.302A>T",
"hgvs_p": "p.Tyr101Phe",
"transcript": "NM_017457.6",
"protein_id": "NP_059431.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 400,
"cds_start": 302,
"cds_end": null,
"cds_length": 1203,
"cdna_start": 441,
"cdna_end": null,
"cdna_length": 4446,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYTH2",
"gene_hgnc_id": 9502,
"hgvs_c": "c.302A>T",
"hgvs_p": "p.Tyr101Phe",
"transcript": "ENST00000641098.1",
"protein_id": "ENSP00000493357.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 400,
"cds_start": 302,
"cds_end": null,
"cds_length": 1203,
"cdna_start": 377,
"cdna_end": null,
"cdna_length": 2721,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYTH2",
"gene_hgnc_id": 9502,
"hgvs_c": "c.302A>T",
"hgvs_p": "p.Tyr101Phe",
"transcript": "ENST00000460595.5",
"protein_id": "ENSP00000493227.1",
"transcript_support_level": 3,
"aa_start": 101,
"aa_end": null,
"aa_length": 273,
"cds_start": 302,
"cds_end": null,
"cds_length": 824,
"cdna_start": 504,
"cdna_end": null,
"cdna_length": 1026,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYTH2",
"gene_hgnc_id": 9502,
"hgvs_c": "c.368A>T",
"hgvs_p": "p.Tyr123Phe",
"transcript": "ENST00000325139.9",
"protein_id": "ENSP00000314566.5",
"transcript_support_level": 2,
"aa_start": 123,
"aa_end": null,
"aa_length": 253,
"cds_start": 368,
"cds_end": null,
"cds_length": 762,
"cdna_start": 693,
"cdna_end": null,
"cdna_length": 1087,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYTH2",
"gene_hgnc_id": 9502,
"hgvs_c": "c.41A>T",
"hgvs_p": "p.Tyr14Phe",
"transcript": "ENST00000595765.2",
"protein_id": "ENSP00000472602.1",
"transcript_support_level": 2,
"aa_start": 14,
"aa_end": null,
"aa_length": 214,
"cds_start": 41,
"cds_end": null,
"cds_length": 645,
"cdna_start": 41,
"cdna_end": null,
"cdna_length": 746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYTH2",
"gene_hgnc_id": 9502,
"hgvs_c": "c.368A>T",
"hgvs_p": "p.Tyr123Phe",
"transcript": "XM_006723472.3",
"protein_id": "XP_006723535.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 421,
"cds_start": 368,
"cds_end": null,
"cds_length": 1266,
"cdna_start": 688,
"cdna_end": null,
"cdna_length": 4690,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYTH2",
"gene_hgnc_id": 9502,
"hgvs_c": "c.368A>T",
"hgvs_p": "p.Tyr123Phe",
"transcript": "XM_047439682.1",
"protein_id": "XP_047295638.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 421,
"cds_start": 368,
"cds_end": null,
"cds_length": 1266,
"cdna_start": 688,
"cdna_end": null,
"cdna_length": 4029,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYTH2",
"gene_hgnc_id": 9502,
"hgvs_c": "c.302A>T",
"hgvs_p": "p.Tyr101Phe",
"transcript": "XM_047439683.1",
"protein_id": "XP_047295639.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 399,
"cds_start": 302,
"cds_end": null,
"cds_length": 1200,
"cdna_start": 441,
"cdna_end": null,
"cdna_length": 3782,
"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": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYTH2",
"gene_hgnc_id": 9502,
"hgvs_c": "n.302A>T",
"hgvs_p": null,
"transcript": "ENST00000391881.7",
"protein_id": "ENSP00000375753.3",
"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": 1546,
"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": "CYTH2",
"gene_hgnc_id": 9502,
"hgvs_c": "n.392A>T",
"hgvs_p": null,
"transcript": "ENST00000462117.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 540,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYTH2",
"gene_hgnc_id": 9502,
"hgvs_c": "n.445A>T",
"hgvs_p": null,
"transcript": "ENST00000474049.1",
"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": 576,
"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": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CYTH2",
"gene_hgnc_id": 9502,
"hgvs_c": "n.463A>T",
"hgvs_p": null,
"transcript": "ENST00000493260.5",
"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": 4652,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CYTH2",
"gene_hgnc_id": 9502,
"dbsnp": null,
"frequency_reference_population": 0.0000054730945,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000547309,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5388091206550598,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.2,
"revel_prediction": "Benign",
"alphamissense_score": 0.1721,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.33,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.314,
"phylop100way_prediction": "Pathogenic",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004228.7",
"gene_symbol": "CYTH2",
"hgnc_id": 9502,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.302A>T",
"hgvs_p": "p.Tyr101Phe"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000595676.1",
"gene_symbol": "ENSG00000268465",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.254A>T",
"hgvs_p": "p.Tyr85Phe"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}