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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: 1-235809917-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=235809917&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 235809917,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000081.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Ser301Gly",
"transcript": "NM_000081.4",
"protein_id": "NP_000072.2",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 3801,
"cds_start": 901,
"cds_end": null,
"cds_length": 11406,
"cdna_start": 1062,
"cdna_end": null,
"cdna_length": 13466,
"mane_select": "ENST00000389793.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Ser301Gly",
"transcript": "ENST00000389793.7",
"protein_id": "ENSP00000374443.2",
"transcript_support_level": 5,
"aa_start": 301,
"aa_end": null,
"aa_length": 3801,
"cds_start": 901,
"cds_end": null,
"cds_length": 11406,
"cdna_start": 1062,
"cdna_end": null,
"cdna_length": 13466,
"mane_select": "NM_000081.4",
"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": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.1452A>G",
"hgvs_p": null,
"transcript": "ENST00000465349.5",
"protein_id": null,
"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": 5220,
"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": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.901A>G",
"hgvs_p": null,
"transcript": "ENST00000489585.5",
"protein_id": "ENSP00000513166.1",
"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": 7069,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Ser301Gly",
"transcript": "NM_001301365.1",
"protein_id": "NP_001288294.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 3801,
"cds_start": 901,
"cds_end": null,
"cds_length": 11406,
"cdna_start": 1520,
"cdna_end": null,
"cdna_length": 13934,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.304A>G",
"hgvs_p": "p.Ser102Gly",
"transcript": "ENST00000697242.1",
"protein_id": "ENSP00000513207.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 1265,
"cds_start": 304,
"cds_end": null,
"cds_length": 3798,
"cdna_start": 444,
"cdna_end": null,
"cdna_length": 3938,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Ser301Gly",
"transcript": "XM_011544031.2",
"protein_id": "XP_011542333.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 3855,
"cds_start": 901,
"cds_end": null,
"cds_length": 11568,
"cdna_start": 1062,
"cdna_end": null,
"cdna_length": 13638,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Ser301Gly",
"transcript": "XM_011544032.2",
"protein_id": "XP_011542334.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 3855,
"cds_start": 901,
"cds_end": null,
"cds_length": 11568,
"cdna_start": 1525,
"cdna_end": null,
"cdna_length": 14101,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Ser301Gly",
"transcript": "XM_011544033.3",
"protein_id": "XP_011542335.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 3855,
"cds_start": 901,
"cds_end": null,
"cds_length": 11568,
"cdna_start": 2849,
"cdna_end": null,
"cdna_length": 15425,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Ser301Gly",
"transcript": "XM_047443026.1",
"protein_id": "XP_047298982.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 3855,
"cds_start": 901,
"cds_end": null,
"cds_length": 11568,
"cdna_start": 7941,
"cdna_end": null,
"cdna_length": 20517,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Ser301Gly",
"transcript": "XM_011544035.3",
"protein_id": "XP_011542337.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 3318,
"cds_start": 901,
"cds_end": null,
"cds_length": 9957,
"cdna_start": 1062,
"cdna_end": null,
"cdna_length": 10323,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Ser301Gly",
"transcript": "XM_047443027.1",
"protein_id": "XP_047298983.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 3264,
"cds_start": 901,
"cds_end": null,
"cds_length": 9795,
"cdna_start": 1062,
"cdna_end": null,
"cdna_length": 10161,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Ser301Gly",
"transcript": "XM_011544037.3",
"protein_id": "XP_011542339.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 2876,
"cds_start": 901,
"cds_end": null,
"cds_length": 8631,
"cdna_start": 1062,
"cdna_end": null,
"cdna_length": 13948,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Ser301Gly",
"transcript": "XM_047443038.1",
"protein_id": "XP_047298994.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 2842,
"cds_start": 901,
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"cdna_start": 1062,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "S",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Ser301Gly",
"transcript": "XM_047443040.1",
"protein_id": "XP_047298996.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 2822,
"cds_start": 901,
"cds_end": null,
"cds_length": 8469,
"cdna_start": 1062,
"cdna_end": null,
"cdna_length": 13786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Ser301Gly",
"transcript": "XM_047443046.1",
"protein_id": "XP_047299002.1",
"transcript_support_level": null,
"aa_start": 301,
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"aa_length": 2788,
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"cdna_start": 1062,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Ser301Gly",
"transcript": "XM_011544039.3",
"protein_id": "XP_011542341.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 2555,
"cds_start": 901,
"cds_end": null,
"cds_length": 7668,
"cdna_start": 1062,
"cdna_end": null,
"cdna_length": 7939,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Ser301Gly",
"transcript": "XM_047443064.1",
"protein_id": "XP_047299020.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 2009,
"cds_start": 901,
"cds_end": null,
"cds_length": 6030,
"cdna_start": 1062,
"cdna_end": null,
"cdna_length": 6286,
"mane_select": null,
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"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": 5,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "n.901A>G",
"hgvs_p": null,
"transcript": "ENST00000697178.1",
"protein_id": "ENSP00000513163.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.-1813A>G",
"hgvs_p": null,
"transcript": "XM_011544036.3",
"protein_id": "XP_011542338.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3076,
"cds_start": -4,
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"cds_length": 9231,
"cdna_start": null,
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"cdna_length": 13570,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"hgvs_c": "c.-1813A>G",
"hgvs_p": null,
"transcript": "XM_047443034.1",
"protein_id": "XP_047298990.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3022,
"cds_start": -4,
"cds_end": null,
"cds_length": 9069,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 13408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LYST",
"gene_hgnc_id": 1968,
"dbsnp": "rs757860752",
"frequency_reference_population": 0.000023261064,
"hom_count_reference_population": 0,
"allele_count_reference_population": 34,
"gnomad_exomes_af": 0.0000232611,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 34,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.014883160591125488,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.02,
"revel_prediction": "Benign",
"alphamissense_score": 0.0695,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.788,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BS1_Supporting",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS1_Supporting"
],
"verdict": "Likely_benign",
"transcript": "NM_000081.4",
"gene_symbol": "LYST",
"hgnc_id": 1968,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Ser301Gly"
}
],
"clinvar_disease": "Chédiak-Higashi syndrome,Inborn genetic diseases,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:5",
"phenotype_combined": "Chédiak-Higashi syndrome|not provided|not specified|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}