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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: X-100833191-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=100833191&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"PP2",
"BP4_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CSTF2",
"hgnc_id": 2484,
"hgvs_c": "c.1279C>T",
"hgvs_p": "p.Pro427Ser",
"inheritance_mode": "XL",
"pathogenic_score": 1,
"score": -5,
"transcript": "NM_001306206.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP2,BP4_Moderate,BS2",
"acmg_score": -5,
"allele_count_reference_population": 32,
"alphamissense_prediction": null,
"alphamissense_score": 0.0692,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.64,
"chr": "X",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.12025490403175354,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 577,
"aa_ref": "P",
"aa_start": 407,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2570,
"cdna_start": 1245,
"cds_end": null,
"cds_length": 1734,
"cds_start": 1219,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001325.3",
"gene_hgnc_id": 2484,
"gene_symbol": "CSTF2",
"hgvs_c": "c.1219C>T",
"hgvs_p": "p.Pro407Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000372972.7",
"protein_coding": true,
"protein_id": "NP_001316.1",
"strand": true,
"transcript": "NM_001325.3",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 577,
"aa_ref": "P",
"aa_start": 407,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2570,
"cdna_start": 1245,
"cds_end": null,
"cds_length": 1734,
"cds_start": 1219,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000372972.7",
"gene_hgnc_id": 2484,
"gene_symbol": "CSTF2",
"hgvs_c": "c.1219C>T",
"hgvs_p": "p.Pro407Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001325.3",
"protein_coding": true,
"protein_id": "ENSP00000362063.2",
"strand": true,
"transcript": "ENST00000372972.7",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 597,
"aa_ref": "P",
"aa_start": 427,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2630,
"cdna_start": 1305,
"cds_end": null,
"cds_length": 1794,
"cds_start": 1279,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000415585.7",
"gene_hgnc_id": 2484,
"gene_symbol": "CSTF2",
"hgvs_c": "c.1279C>T",
"hgvs_p": "p.Pro427Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000387996.2",
"strand": true,
"transcript": "ENST00000415585.7",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 626,
"aa_ref": "P",
"aa_start": 456,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2720,
"cdna_start": 1392,
"cds_end": null,
"cds_length": 1881,
"cds_start": 1366,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000866722.1",
"gene_hgnc_id": 2484,
"gene_symbol": "CSTF2",
"hgvs_c": "c.1366C>T",
"hgvs_p": "p.Pro456Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000536781.1",
"strand": true,
"transcript": "ENST00000866722.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 626,
"aa_ref": "P",
"aa_start": 456,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2345,
"cdna_start": 1395,
"cds_end": null,
"cds_length": 1881,
"cds_start": 1366,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000948101.1",
"gene_hgnc_id": 2484,
"gene_symbol": "CSTF2",
"hgvs_c": "c.1366C>T",
"hgvs_p": "p.Pro456Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000618160.1",
"strand": true,
"transcript": "ENST00000948101.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 609,
"aa_ref": "P",
"aa_start": 439,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2084,
"cdna_start": 1344,
"cds_end": null,
"cds_length": 1830,
"cds_start": 1315,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000924425.1",
"gene_hgnc_id": 2484,
"gene_symbol": "CSTF2",
"hgvs_c": "c.1315C>T",
"hgvs_p": "p.Pro439Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594484.1",
"strand": true,
"transcript": "ENST00000924425.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 597,
"aa_ref": "P",
"aa_start": 427,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2630,
"cdna_start": 1305,
"cds_end": null,
"cds_length": 1794,
"cds_start": 1279,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_001306206.2",
"gene_hgnc_id": 2484,
"gene_symbol": "CSTF2",
"hgvs_c": "c.1279C>T",
"hgvs_p": "p.Pro427Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001293135.1",
"strand": true,
"transcript": "NM_001306206.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 597,
"aa_ref": "P",
"aa_start": 427,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2233,
"cdna_start": 1285,
"cds_end": null,
"cds_length": 1794,
"cds_start": 1279,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000924426.1",
"gene_hgnc_id": 2484,
"gene_symbol": "CSTF2",
"hgvs_c": "c.1279C>T",
"hgvs_p": "p.Pro427Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594485.1",
"strand": true,
"transcript": "ENST00000924426.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 580,
"aa_ref": "P",
"aa_start": 410,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1963,
"cdna_start": 1242,
"cds_end": null,
"cds_length": 1743,
"cds_start": 1228,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000948100.1",
"gene_hgnc_id": 2484,
"gene_symbol": "CSTF2",
"hgvs_c": "c.1228C>T",
"hgvs_p": "p.Pro410Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000618159.1",
"strand": true,
"transcript": "ENST00000948100.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 577,
"aa_ref": "P",
"aa_start": 407,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2217,
"cdna_start": 1267,
"cds_end": null,
"cds_length": 1734,
"cds_start": 1219,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000866724.1",
"gene_hgnc_id": 2484,
"gene_symbol": "CSTF2",
"hgvs_c": "c.1219C>T",
"hgvs_p": "p.Pro407Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000536783.1",
"strand": true,
"transcript": "ENST00000866724.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 576,
"aa_ref": "P",
"aa_start": 406,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1992,
"cdna_start": 1249,
"cds_end": null,
"cds_length": 1731,
"cds_start": 1216,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000924424.1",
"gene_hgnc_id": 2484,
"gene_symbol": "CSTF2",
"hgvs_c": "c.1216C>T",
"hgvs_p": "p.Pro406Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594483.1",
"strand": true,
"transcript": "ENST00000924424.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 560,
"aa_ref": "P",
"aa_start": 390,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2519,
"cdna_start": 1194,
"cds_end": null,
"cds_length": 1683,
"cds_start": 1168,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001306209.2",
"gene_hgnc_id": 2484,
"gene_symbol": "CSTF2",
"hgvs_c": "c.1168C>T",
"hgvs_p": "p.Pro390Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001293138.1",
"strand": true,
"transcript": "NM_001306209.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 560,
"aa_ref": "P",
"aa_start": 390,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2505,
"cdna_start": 1204,
"cds_end": null,
"cds_length": 1683,
"cds_start": 1168,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000866723.1",
"gene_hgnc_id": 2484,
"gene_symbol": "CSTF2",
"hgvs_c": "c.1168C>T",
"hgvs_p": "p.Pro390Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000536782.1",
"strand": true,
"transcript": "ENST00000866723.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1693,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000475126.5",
"gene_hgnc_id": 2484,
"gene_symbol": "CSTF2",
"hgvs_c": "n.1168C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000432060.1",
"strand": true,
"transcript": "ENST00000475126.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs984214617",
"effect": "missense_variant",
"frequency_reference_population": 0.000026497393,
"gene_hgnc_id": 2484,
"gene_symbol": "CSTF2",
"gnomad_exomes_ac": 28,
"gnomad_exomes_af": 0.0000255583,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.0000356719,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 11,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.474,
"pos": 100833191,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.076,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001306206.2"
}
]
}