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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: 21-46431579-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=46431579&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "21",
"pos": 46431579,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_006031.6",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "c.8115C>T",
"hgvs_p": "p.Cys2705Cys",
"transcript": "NM_006031.6",
"protein_id": "NP_006022.3",
"transcript_support_level": null,
"aa_start": 2705,
"aa_end": null,
"aa_length": 3336,
"cds_start": 8115,
"cds_end": null,
"cds_length": 10011,
"cdna_start": 8188,
"cdna_end": null,
"cdna_length": 10526,
"mane_select": "ENST00000359568.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "c.8115C>T",
"hgvs_p": "p.Cys2705Cys",
"transcript": "ENST00000359568.10",
"protein_id": "ENSP00000352572.5",
"transcript_support_level": 1,
"aa_start": 2705,
"aa_end": null,
"aa_length": 3336,
"cds_start": 8115,
"cds_end": null,
"cds_length": 10011,
"cdna_start": 8188,
"cdna_end": null,
"cdna_length": 10526,
"mane_select": "NM_006031.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "c.7761C>T",
"hgvs_p": "p.Cys2587Cys",
"transcript": "ENST00000480896.5",
"protein_id": "ENSP00000511989.1",
"transcript_support_level": 1,
"aa_start": 2587,
"aa_end": null,
"aa_length": 3139,
"cds_start": 7761,
"cds_end": null,
"cds_length": 9420,
"cdna_start": 8384,
"cdna_end": null,
"cdna_length": 10485,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 39,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "c.8148C>T",
"hgvs_p": "p.Cys2716Cys",
"transcript": "ENST00000695558.1",
"protein_id": "ENSP00000512015.1",
"transcript_support_level": null,
"aa_start": 2716,
"aa_end": null,
"aa_length": 3347,
"cds_start": 8148,
"cds_end": null,
"cds_length": 10044,
"cdna_start": 8221,
"cdna_end": null,
"cdna_length": 10559,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "c.7761C>T",
"hgvs_p": "p.Cys2587Cys",
"transcript": "NM_001315529.2",
"protein_id": "NP_001302458.1",
"transcript_support_level": null,
"aa_start": 2587,
"aa_end": null,
"aa_length": 3139,
"cds_start": 7761,
"cds_end": null,
"cds_length": 9420,
"cdna_start": 8605,
"cdna_end": null,
"cdna_length": 10706,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "c.2148C>T",
"hgvs_p": "p.Cys716Cys",
"transcript": "ENST00000695528.1",
"protein_id": "ENSP00000511990.1",
"transcript_support_level": null,
"aa_start": 716,
"aa_end": null,
"aa_length": 1347,
"cds_start": 2148,
"cds_end": null,
"cds_length": 4044,
"cdna_start": 2148,
"cdna_end": null,
"cdna_length": 4468,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "c.933C>T",
"hgvs_p": "p.Cys311Cys",
"transcript": "ENST00000418394.2",
"protein_id": "ENSP00000404708.2",
"transcript_support_level": 3,
"aa_start": 311,
"aa_end": null,
"aa_length": 774,
"cds_start": 933,
"cds_end": null,
"cds_length": 2325,
"cdna_start": 934,
"cdna_end": null,
"cdna_length": 2689,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "c.933C>T",
"hgvs_p": "p.Cys311Cys",
"transcript": "ENST00000695530.1",
"protein_id": "ENSP00000511991.1",
"transcript_support_level": null,
"aa_start": 311,
"aa_end": null,
"aa_length": 746,
"cds_start": 933,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 934,
"cdna_end": null,
"cdna_length": 2662,
"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": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "n.122C>T",
"hgvs_p": null,
"transcript": "ENST00000482575.1",
"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": 578,
"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": 11,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "n.2460C>T",
"hgvs_p": null,
"transcript": "ENST00000695527.1",
"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": 6761,
"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": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "n.2148C>T",
"hgvs_p": null,
"transcript": "ENST00000695529.1",
"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": 4976,
"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": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "n.1717C>T",
"hgvs_p": null,
"transcript": "ENST00000695531.1",
"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": 4037,
"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": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "n.1717C>T",
"hgvs_p": null,
"transcript": "ENST00000695532.1",
"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": 3771,
"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": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "n.785C>T",
"hgvs_p": null,
"transcript": "ENST00000695533.1",
"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": 3105,
"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": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "n.746C>T",
"hgvs_p": null,
"transcript": "ENST00000695534.1",
"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": 3574,
"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": 40,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "n.*7358C>T",
"hgvs_p": null,
"transcript": "ENST00000703224.1",
"protein_id": "ENSP00000515242.1",
"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": 10699,
"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": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "n.785C>T",
"hgvs_p": null,
"transcript": "ENST00000703226.1",
"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": 3105,
"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": 40,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"hgvs_c": "n.*7358C>T",
"hgvs_p": null,
"transcript": "ENST00000703224.1",
"protein_id": "ENSP00000515242.1",
"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": 10699,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PCNT",
"gene_hgnc_id": 16068,
"dbsnp": "rs756904669",
"frequency_reference_population": 0.000021685844,
"hom_count_reference_population": 0,
"allele_count_reference_population": 35,
"gnomad_exomes_af": 0.00002326,
"gnomad_genomes_af": 0.00000656961,
"gnomad_exomes_ac": 34,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7900000214576721,
"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": -0.79,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.463,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7"
],
"verdict": "Benign",
"transcript": "NM_006031.6",
"gene_symbol": "PCNT",
"hgnc_id": 16068,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.8115C>T",
"hgvs_p": "p.Cys2705Cys"
}
],
"clinvar_disease": "PCNT-related disorder,not provided,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "not specified|PCNT-related disorder|not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}