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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: 3-38896891-AATG-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=38896891&ref=AATG&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 38896891,
"ref": "AATG",
"alt": "A",
"effect": "disruptive_inframe_deletion",
"transcript": "ENST00000302328.9",
"consequences": [
{
"aa_ref": "SL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.2354_2356delCAT",
"hgvs_p": "p.Ser785del",
"transcript": "NM_001349253.2",
"protein_id": "NP_001336182.1",
"transcript_support_level": null,
"aa_start": 785,
"aa_end": null,
"aa_length": 1791,
"cds_start": 2354,
"cds_end": null,
"cds_length": 5376,
"cdna_start": 2843,
"cdna_end": null,
"cdna_length": 6793,
"mane_select": "ENST00000302328.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SL",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.2354_2356delCAT",
"hgvs_p": "p.Ser785del",
"transcript": "ENST00000302328.9",
"protein_id": "ENSP00000307599.3",
"transcript_support_level": 5,
"aa_start": 785,
"aa_end": null,
"aa_length": 1791,
"cds_start": 2354,
"cds_end": null,
"cds_length": 5376,
"cdna_start": 2843,
"cdna_end": null,
"cdna_length": 6793,
"mane_select": "NM_001349253.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.2354_2356delCAT",
"hgvs_p": "p.Ser785del",
"transcript": "NM_014139.3",
"protein_id": "NP_054858.2",
"transcript_support_level": null,
"aa_start": 785,
"aa_end": null,
"aa_length": 1791,
"cds_start": 2354,
"cds_end": null,
"cds_length": 5376,
"cdna_start": 2555,
"cdna_end": null,
"cdna_length": 6505,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.2354_2356delCAT",
"hgvs_p": "p.Ser785del",
"transcript": "ENST00000668754.1",
"protein_id": "ENSP00000499569.1",
"transcript_support_level": null,
"aa_start": 785,
"aa_end": null,
"aa_length": 1791,
"cds_start": 2354,
"cds_end": null,
"cds_length": 5376,
"cdna_start": 3340,
"cdna_end": null,
"cdna_length": 7285,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.2354_2356delCAT",
"hgvs_p": "p.Ser785del",
"transcript": "ENST00000456224.7",
"protein_id": "ENSP00000416757.3",
"transcript_support_level": 5,
"aa_start": 785,
"aa_end": null,
"aa_length": 1753,
"cds_start": 2354,
"cds_end": null,
"cds_length": 5262,
"cdna_start": 2356,
"cdna_end": null,
"cdna_length": 5262,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.2174_2176delCAT",
"hgvs_p": "p.Ser725del",
"transcript": "ENST00000675892.1",
"protein_id": "ENSP00000502318.1",
"transcript_support_level": null,
"aa_start": 725,
"aa_end": null,
"aa_length": 1731,
"cds_start": 2174,
"cds_end": null,
"cds_length": 5196,
"cdna_start": 2176,
"cdna_end": null,
"cdna_length": 5196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.2354_2356delCAT",
"hgvs_p": "p.Ser785del",
"transcript": "ENST00000444237.2",
"protein_id": "ENSP00000408028.2",
"transcript_support_level": 5,
"aa_start": 785,
"aa_end": null,
"aa_length": 1444,
"cds_start": 2354,
"cds_end": null,
"cds_length": 4335,
"cdna_start": 2555,
"cdna_end": null,
"cdna_length": 5729,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.2729_2731delCAT",
"hgvs_p": "p.Ser910del",
"transcript": "XM_047447378.1",
"protein_id": "XP_047303334.1",
"transcript_support_level": null,
"aa_start": 910,
"aa_end": null,
"aa_length": 1916,
"cds_start": 2729,
"cds_end": null,
"cds_length": 5751,
"cdna_start": 2957,
"cdna_end": null,
"cdna_length": 6907,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.2354_2356delCAT",
"hgvs_p": "p.Ser785del",
"transcript": "XM_017005650.2",
"protein_id": "XP_016861139.1",
"transcript_support_level": null,
"aa_start": 785,
"aa_end": null,
"aa_length": 1791,
"cds_start": 2354,
"cds_end": null,
"cds_length": 5376,
"cdna_start": 2724,
"cdna_end": null,
"cdna_length": 6674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.2081_2083delCAT",
"hgvs_p": "p.Ser694del",
"transcript": "XM_017005651.2",
"protein_id": "XP_016861140.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 1700,
"cds_start": 2081,
"cds_end": null,
"cds_length": 5103,
"cdna_start": 2599,
"cdna_end": null,
"cdna_length": 6549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.1691_1693delCAT",
"hgvs_p": "p.Ser564del",
"transcript": "XM_011533321.3",
"protein_id": "XP_011531623.1",
"transcript_support_level": null,
"aa_start": 564,
"aa_end": null,
"aa_length": 1570,
"cds_start": 1691,
"cds_end": null,
"cds_length": 4713,
"cdna_start": 1780,
"cdna_end": null,
"cdna_length": 5730,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.758_760delCAT",
"hgvs_p": "p.Ser253del",
"transcript": "XM_017005653.2",
"protein_id": "XP_016861142.1",
"transcript_support_level": null,
"aa_start": 253,
"aa_end": null,
"aa_length": 1259,
"cds_start": 758,
"cds_end": null,
"cds_length": 3780,
"cdna_start": 1178,
"cdna_end": null,
"cdna_length": 5128,
"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": 14,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "n.2354_2356delCAT",
"hgvs_p": null,
"transcript": "ENST00000675223.1",
"protein_id": "ENSP00000502481.1",
"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": 5455,
"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": 14,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "n.2354_2356delCAT",
"hgvs_p": null,
"transcript": "ENST00000675672.1",
"protein_id": "ENSP00000502446.1",
"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": 5430,
"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": 15,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "n.*2071_*2073delCAT",
"hgvs_p": null,
"transcript": "ENST00000676045.1",
"protein_id": "ENSP00000501685.1",
"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": 5420,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "n.*2071_*2073delCAT",
"hgvs_p": null,
"transcript": "ENST00000676045.1",
"protein_id": "ENSP00000501685.1",
"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": 5420,
"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": 25,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"hgvs_c": "c.2023-1930_2023-1928delCAT",
"hgvs_p": null,
"transcript": "ENST00000676176.1",
"protein_id": "ENSP00000501891.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1664,
"cds_start": -4,
"cds_end": null,
"cds_length": 4995,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4995,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SCN11A",
"gene_hgnc_id": 10583,
"dbsnp": "rs757197374",
"frequency_reference_population": 0.000006821858,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000616054,
"gnomad_genomes_af": 0.0000131966,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": -0.057,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.06,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM4_Supporting,BS2",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PM4_Supporting",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000302328.9",
"gene_symbol": "SCN11A",
"hgnc_id": 10583,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2354_2356delCAT",
"hgvs_p": "p.Ser785del"
}
],
"clinvar_disease": "Familial episodic pain syndrome with predominantly lower limb involvement,Hereditary sensory and autonomic neuropathy type 7",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Hereditary sensory and autonomic neuropathy type 7;Familial episodic pain syndrome with predominantly lower limb involvement",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}