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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: 3-47124136-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=47124136&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 47124136,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000409792.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "c.500C>T",
"hgvs_p": "p.Pro167Leu",
"transcript": "NM_014159.7",
"protein_id": "NP_054878.5",
"transcript_support_level": null,
"aa_start": 167,
"aa_end": null,
"aa_length": 2564,
"cds_start": 500,
"cds_end": null,
"cds_length": 7695,
"cdna_start": 689,
"cdna_end": null,
"cdna_length": 8541,
"mane_select": "ENST00000409792.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "c.500C>T",
"hgvs_p": "p.Pro167Leu",
"transcript": "ENST00000409792.4",
"protein_id": "ENSP00000386759.3",
"transcript_support_level": 5,
"aa_start": 167,
"aa_end": null,
"aa_length": 2564,
"cds_start": 500,
"cds_end": null,
"cds_length": 7695,
"cdna_start": 689,
"cdna_end": null,
"cdna_length": 8541,
"mane_select": "NM_014159.7",
"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": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "n.113C>T",
"hgvs_p": null,
"transcript": "ENST00000330022.11",
"protein_id": "ENSP00000332415.7",
"transcript_support_level": 1,
"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": 8172,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "c.368C>T",
"hgvs_p": "p.Pro123Leu",
"transcript": "NM_001349370.3",
"protein_id": "NP_001336299.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 2520,
"cds_start": 368,
"cds_end": null,
"cds_length": 7563,
"cdna_start": 673,
"cdna_end": null,
"cdna_length": 8525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "c.368C>T",
"hgvs_p": "p.Pro123Leu",
"transcript": "ENST00000638947.2",
"protein_id": "ENSP00000491413.2",
"transcript_support_level": 5,
"aa_start": 123,
"aa_end": null,
"aa_length": 2520,
"cds_start": 368,
"cds_end": null,
"cds_length": 7563,
"cdna_start": 442,
"cdna_end": null,
"cdna_length": 8302,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "c.401C>T",
"hgvs_p": "p.Pro134Leu",
"transcript": "ENST00000685005.1",
"protein_id": "ENSP00000509568.1",
"transcript_support_level": null,
"aa_start": 134,
"aa_end": null,
"aa_length": 2486,
"cds_start": 401,
"cds_end": null,
"cds_length": 7461,
"cdna_start": 401,
"cdna_end": null,
"cdna_length": 8109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "c.368C>T",
"hgvs_p": "p.Pro123Leu",
"transcript": "ENST00000412450.1",
"protein_id": "ENSP00000416401.1",
"transcript_support_level": 2,
"aa_start": 123,
"aa_end": null,
"aa_length": 1339,
"cds_start": 368,
"cds_end": null,
"cds_length": 4021,
"cdna_start": 578,
"cdna_end": null,
"cdna_length": 4231,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "c.368C>T",
"hgvs_p": "p.Pro123Leu",
"transcript": "XM_047448045.1",
"protein_id": "XP_047304001.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 2520,
"cds_start": 368,
"cds_end": null,
"cds_length": 7563,
"cdna_start": 470,
"cdna_end": null,
"cdna_length": 8322,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "c.368C>T",
"hgvs_p": "p.Pro123Leu",
"transcript": "XM_024453487.2",
"protein_id": "XP_024309255.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 2475,
"cds_start": 368,
"cds_end": null,
"cds_length": 7428,
"cdna_start": 470,
"cdna_end": null,
"cdna_length": 8187,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "c.368C>T",
"hgvs_p": "p.Pro123Leu",
"transcript": "XM_024453488.2",
"protein_id": "XP_024309256.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 2420,
"cds_start": 368,
"cds_end": null,
"cds_length": 7263,
"cdna_start": 429,
"cdna_end": null,
"cdna_length": 7981,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "c.368C>T",
"hgvs_p": "p.Pro123Leu",
"transcript": "XM_024453489.1",
"protein_id": "XP_024309257.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 1633,
"cds_start": 368,
"cds_end": null,
"cds_length": 4902,
"cdna_start": 429,
"cdna_end": null,
"cdna_length": 5065,
"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": 3,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "n.689C>T",
"hgvs_p": null,
"transcript": "NR_146158.3",
"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": 8709,
"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": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "n.429C>T",
"hgvs_p": null,
"transcript": "XR_002959514.2",
"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": 6233,
"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": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "n.429C>T",
"hgvs_p": null,
"transcript": "XR_007095670.1",
"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": 7400,
"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": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "n.429C>T",
"hgvs_p": null,
"transcript": "XR_007095671.1",
"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": 6244,
"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": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "n.429C>T",
"hgvs_p": null,
"transcript": "XR_007095672.1",
"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": 6060,
"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": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "n.470C>T",
"hgvs_p": null,
"transcript": "XR_007095673.1",
"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": 6236,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"hgvs_c": "c.72-26055C>T",
"hgvs_p": null,
"transcript": "ENST00000691544.1",
"protein_id": "ENSP00000510710.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 916,
"cds_start": -4,
"cds_end": null,
"cds_length": 2751,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000296084",
"gene_hgnc_id": null,
"hgvs_c": "n.236-160G>A",
"hgvs_p": null,
"transcript": "ENST00000736255.1",
"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": 543,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SETD2",
"gene_hgnc_id": 18420,
"dbsnp": "rs78682369",
"frequency_reference_population": 0.00044845475,
"hom_count_reference_population": 0,
"allele_count_reference_population": 696,
"gnomad_exomes_af": 0.000471543,
"gnomad_genomes_af": 0.00023632,
"gnomad_exomes_ac": 660,
"gnomad_genomes_ac": 36,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03280913829803467,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.139,
"revel_prediction": "Benign",
"alphamissense_score": 0.0674,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.977,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000409792.4",
"gene_symbol": "SETD2",
"hgnc_id": 18420,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.500C>T",
"hgvs_p": "p.Pro167Leu"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "ENST00000736255.1",
"gene_symbol": "ENSG00000296084",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.236-160G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Luscan-Lumish syndrome,SETD2-related disorder,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:3",
"phenotype_combined": "not provided|Luscan-Lumish syndrome|SETD2-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}