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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-153953629-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153953629&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153953629,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000310441.12",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4475C>G",
"hgvs_p": "p.Pro1492Arg",
"transcript": "NM_005334.3",
"protein_id": "NP_005325.2",
"transcript_support_level": null,
"aa_start": 1492,
"aa_end": null,
"aa_length": 2035,
"cds_start": 4475,
"cds_end": null,
"cds_length": 6108,
"cdna_start": 5453,
"cdna_end": null,
"cdna_length": 8876,
"mane_select": "ENST00000310441.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4475C>G",
"hgvs_p": "p.Pro1492Arg",
"transcript": "ENST00000310441.12",
"protein_id": "ENSP00000309555.7",
"transcript_support_level": 1,
"aa_start": 1492,
"aa_end": null,
"aa_length": 2035,
"cds_start": 4475,
"cds_end": null,
"cds_length": 6108,
"cdna_start": 5453,
"cdna_end": null,
"cdna_length": 8876,
"mane_select": "NM_005334.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4475C>G",
"hgvs_p": "p.Pro1492Arg",
"transcript": "NM_001440843.1",
"protein_id": "NP_001427772.1",
"transcript_support_level": null,
"aa_start": 1492,
"aa_end": null,
"aa_length": 2082,
"cds_start": 4475,
"cds_end": null,
"cds_length": 6249,
"cdna_start": 5453,
"cdna_end": null,
"cdna_length": 9017,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4475C>G",
"hgvs_p": "p.Pro1492Arg",
"transcript": "NM_001410705.1",
"protein_id": "NP_001397634.1",
"transcript_support_level": null,
"aa_start": 1492,
"aa_end": null,
"aa_length": 2080,
"cds_start": 4475,
"cds_end": null,
"cds_length": 6243,
"cdna_start": 5453,
"cdna_end": null,
"cdna_length": 9011,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4475C>G",
"hgvs_p": "p.Pro1492Arg",
"transcript": "ENST00000369984.4",
"protein_id": "ENSP00000359001.4",
"transcript_support_level": 5,
"aa_start": 1492,
"aa_end": null,
"aa_length": 2080,
"cds_start": 4475,
"cds_end": null,
"cds_length": 6243,
"cdna_start": 4819,
"cdna_end": null,
"cdna_length": 8375,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4475C>G",
"hgvs_p": "p.Pro1492Arg",
"transcript": "NM_001440844.1",
"protein_id": "NP_001427773.1",
"transcript_support_level": null,
"aa_start": 1492,
"aa_end": null,
"aa_length": 2079,
"cds_start": 4475,
"cds_end": null,
"cds_length": 6240,
"cdna_start": 5453,
"cdna_end": null,
"cdna_length": 9008,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4475C>G",
"hgvs_p": "p.Pro1492Arg",
"transcript": "NM_001440845.1",
"protein_id": "NP_001427774.1",
"transcript_support_level": null,
"aa_start": 1492,
"aa_end": null,
"aa_length": 2079,
"cds_start": 4475,
"cds_end": null,
"cds_length": 6240,
"cdna_start": 5453,
"cdna_end": null,
"cdna_length": 9008,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4475C>G",
"hgvs_p": "p.Pro1492Arg",
"transcript": "NM_001440846.1",
"protein_id": "NP_001427775.1",
"transcript_support_level": null,
"aa_start": 1492,
"aa_end": null,
"aa_length": 2078,
"cds_start": 4475,
"cds_end": null,
"cds_length": 6237,
"cdna_start": 5453,
"cdna_end": null,
"cdna_length": 9005,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4475C>G",
"hgvs_p": "p.Pro1492Arg",
"transcript": "NM_001440847.1",
"protein_id": "NP_001427776.1",
"transcript_support_level": null,
"aa_start": 1492,
"aa_end": null,
"aa_length": 2039,
"cds_start": 4475,
"cds_end": null,
"cds_length": 6120,
"cdna_start": 5453,
"cdna_end": null,
"cdna_length": 8888,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4475C>G",
"hgvs_p": "p.Pro1492Arg",
"transcript": "NM_001440848.1",
"protein_id": "NP_001427777.1",
"transcript_support_level": null,
"aa_start": 1492,
"aa_end": null,
"aa_length": 2038,
"cds_start": 4475,
"cds_end": null,
"cds_length": 6117,
"cdna_start": 5453,
"cdna_end": null,
"cdna_length": 8885,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4475C>G",
"hgvs_p": "p.Pro1492Arg",
"transcript": "NM_001440849.1",
"protein_id": "NP_001427778.1",
"transcript_support_level": null,
"aa_start": 1492,
"aa_end": null,
"aa_length": 2036,
"cds_start": 4475,
"cds_end": null,
"cds_length": 6111,
"cdna_start": 5453,
"cdna_end": null,
"cdna_length": 8879,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4277C>G",
"hgvs_p": "p.Pro1426Arg",
"transcript": "NM_001440850.1",
"protein_id": "NP_001427779.1",
"transcript_support_level": null,
"aa_start": 1426,
"aa_end": null,
"aa_length": 2013,
"cds_start": 4277,
"cds_end": null,
"cds_length": 6042,
"cdna_start": 5255,
"cdna_end": null,
"cdna_length": 8810,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4277C>G",
"hgvs_p": "p.Pro1426Arg",
"transcript": "NM_001440851.1",
"protein_id": "NP_001427780.1",
"transcript_support_level": null,
"aa_start": 1426,
"aa_end": null,
"aa_length": 1969,
"cds_start": 4277,
"cds_end": null,
"cds_length": 5910,
"cdna_start": 5255,
"cdna_end": null,
"cdna_length": 8678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.197C>G",
"hgvs_p": "p.Pro66Arg",
"transcript": "ENST00000444191.5",
"protein_id": "ENSP00000399589.1",
"transcript_support_level": 5,
"aa_start": 66,
"aa_end": null,
"aa_length": 610,
"cds_start": 197,
"cds_end": null,
"cds_length": 1833,
"cdna_start": 198,
"cdna_end": null,
"cdna_length": 3624,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4475C>G",
"hgvs_p": "p.Pro1492Arg",
"transcript": "XM_047442051.1",
"protein_id": "XP_047298007.1",
"transcript_support_level": null,
"aa_start": 1492,
"aa_end": null,
"aa_length": 2083,
"cds_start": 4475,
"cds_end": null,
"cds_length": 6252,
"cdna_start": 5453,
"cdna_end": null,
"cdna_length": 9020,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4475C>G",
"hgvs_p": "p.Pro1492Arg",
"transcript": "XM_047442053.1",
"protein_id": "XP_047298009.1",
"transcript_support_level": null,
"aa_start": 1492,
"aa_end": null,
"aa_length": 2082,
"cds_start": 4475,
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"cdna_start": 5453,
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"cdna_length": 9017,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4475C>G",
"hgvs_p": "p.Pro1492Arg",
"transcript": "XM_047442054.1",
"protein_id": "XP_047298010.1",
"transcript_support_level": null,
"aa_start": 1492,
"aa_end": null,
"aa_length": 2081,
"cds_start": 4475,
"cds_end": null,
"cds_length": 6246,
"cdna_start": 5453,
"cdna_end": null,
"cdna_length": 9014,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4277C>G",
"hgvs_p": "p.Pro1426Arg",
"transcript": "XM_047442058.1",
"protein_id": "XP_047298014.1",
"transcript_support_level": null,
"aa_start": 1426,
"aa_end": null,
"aa_length": 2017,
"cds_start": 4277,
"cds_end": null,
"cds_length": 6054,
"cdna_start": 5255,
"cdna_end": null,
"cdna_length": 8822,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.4277C>G",
"hgvs_p": "p.Pro1426Arg",
"transcript": "XM_047442059.1",
"protein_id": "XP_047298015.1",
"transcript_support_level": null,
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"aa_end": null,
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"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
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"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"hgvs_c": "c.3566C>G",
"hgvs_p": "p.Pro1189Arg",
"transcript": "XM_047442061.1",
"protein_id": "XP_047298017.1",
"transcript_support_level": null,
"aa_start": 1189,
"aa_end": null,
"aa_length": 1780,
"cds_start": 3566,
"cds_end": null,
"cds_length": 5343,
"cdna_start": 3656,
"cdna_end": null,
"cdna_length": 7223,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HCFC1",
"gene_hgnc_id": 4839,
"dbsnp": "rs782407440",
"frequency_reference_population": 0.000058730642,
"hom_count_reference_population": 21,
"allele_count_reference_population": 71,
"gnomad_exomes_af": 0.0000638447,
"gnomad_genomes_af": 0.00000888897,
"gnomad_exomes_ac": 70,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3691558241844177,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.296,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3564,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.147,
"phylop100way_prediction": "Uncertain_significance",
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BP6,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000310441.12",
"gene_symbol": "HCFC1",
"hgnc_id": 4839,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.4475C>G",
"hgvs_p": "p.Pro1492Arg"
}
],
"clinvar_disease": " type cblX,Methylmalonic acidemia with homocystinuria,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:1",
"phenotype_combined": "not specified|Methylmalonic acidemia with homocystinuria, type cblX",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}