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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: 1-240207641-TCCTCCGCCCCCTCTACCCGGAGCGGCAATACCC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=240207641&ref=TCCTCCGCCCCCTCTACCCGGAGCGGCAATACCC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 240207641,
"ref": "TCCTCCGCCCCCTCTACCCGGAGCGGCAATACCC",
"alt": "T",
"effect": "disruptive_inframe_deletion",
"transcript": "NM_001305424.2",
"consequences": [
{
"aa_ref": "LPGAAIPPPPPL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMN2",
"gene_hgnc_id": 14074,
"hgvs_c": "c.2844_2876delACCCGGAGCGGCAATACCCCCTCCGCCCCCTCT",
"hgvs_p": "p.Pro949_Leu959del",
"transcript": "NM_020066.5",
"protein_id": "NP_064450.3",
"transcript_support_level": null,
"aa_start": 948,
"aa_end": null,
"aa_length": 1722,
"cds_start": 2844,
"cds_end": null,
"cds_length": 5169,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000319653.14",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020066.5"
},
{
"aa_ref": "LPGAAIPPPPPL",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMN2",
"gene_hgnc_id": 14074,
"hgvs_c": "c.2844_2876delACCCGGAGCGGCAATACCCCCTCCGCCCCCTCT",
"hgvs_p": "p.Pro949_Leu959del",
"transcript": "ENST00000319653.14",
"protein_id": "ENSP00000318884.9",
"transcript_support_level": 5,
"aa_start": 948,
"aa_end": null,
"aa_length": 1722,
"cds_start": 2844,
"cds_end": null,
"cds_length": 5169,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_020066.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000319653.14"
},
{
"aa_ref": "LPGAAIPPPPPL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMN2",
"gene_hgnc_id": 14074,
"hgvs_c": "c.2856_2888delACCCGGAGCGGCAATACCCCCTCCGCCCCCTCT",
"hgvs_p": "p.Pro953_Leu963del",
"transcript": "NM_001305424.2",
"protein_id": "NP_001292353.1",
"transcript_support_level": null,
"aa_start": 952,
"aa_end": null,
"aa_length": 1726,
"cds_start": 2856,
"cds_end": null,
"cds_length": 5181,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001305424.2"
},
{
"aa_ref": "LPGAAIPPPPPL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMN2",
"gene_hgnc_id": 14074,
"hgvs_c": "c.2856_2888delACCCGGAGCGGCAATACCCCCTCCGCCCCCTCT",
"hgvs_p": "p.Pro953_Leu963del",
"transcript": "XM_017001837.2",
"protein_id": "XP_016857326.1",
"transcript_support_level": null,
"aa_start": 952,
"aa_end": null,
"aa_length": 1417,
"cds_start": 2856,
"cds_end": null,
"cds_length": 4254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001837.2"
},
{
"aa_ref": "LPGAAIPPPPPL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMN2",
"gene_hgnc_id": 14074,
"hgvs_c": "c.2856_2888delACCCGGAGCGGCAATACCCCCTCCGCCCCCTCT",
"hgvs_p": "p.Pro953_Leu963del",
"transcript": "XM_017001838.2",
"protein_id": "XP_016857327.1",
"transcript_support_level": null,
"aa_start": 952,
"aa_end": null,
"aa_length": 1384,
"cds_start": 2856,
"cds_end": null,
"cds_length": 4155,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001838.2"
},
{
"aa_ref": "LPGAAIPPPPPL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMN2",
"gene_hgnc_id": 14074,
"hgvs_c": "c.2856_2888delACCCGGAGCGGCAATACCCCCTCCGCCCCCTCT",
"hgvs_p": "p.Pro953_Leu963del",
"transcript": "XM_011544237.4",
"protein_id": "XP_011542539.1",
"transcript_support_level": null,
"aa_start": 952,
"aa_end": null,
"aa_length": 1360,
"cds_start": 2856,
"cds_end": null,
"cds_length": 4083,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011544237.4"
},
{
"aa_ref": "LPGAAIPPPPPL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMN2",
"gene_hgnc_id": 14074,
"hgvs_c": "c.2844_2876delACCCGGAGCGGCAATACCCCCTCCGCCCCCTCT",
"hgvs_p": "p.Pro949_Leu959del",
"transcript": "XM_047425620.1",
"protein_id": "XP_047281576.1",
"transcript_support_level": null,
"aa_start": 948,
"aa_end": null,
"aa_length": 1356,
"cds_start": 2844,
"cds_end": null,
"cds_length": 4071,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047425620.1"
},
{
"aa_ref": "LPGAAIPPPPPL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMN2",
"gene_hgnc_id": 14074,
"hgvs_c": "c.984_1016delACCCGGAGCGGCAATACCCCCTCCGCCCCCTCT",
"hgvs_p": "p.Pro329_Leu339del",
"transcript": "XM_017001840.3",
"protein_id": "XP_016857329.1",
"transcript_support_level": null,
"aa_start": 328,
"aa_end": null,
"aa_length": 1102,
"cds_start": 984,
"cds_end": null,
"cds_length": 3309,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001840.3"
},
{
"aa_ref": "LPGAAIPPPPPL",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FMN2",
"gene_hgnc_id": 14074,
"hgvs_c": "c.984_1016delACCCGGAGCGGCAATACCCCCTCCGCCCCCTCT",
"hgvs_p": "p.Pro329_Leu339del",
"transcript": "XM_017001841.3",
"protein_id": "XP_016857330.1",
"transcript_support_level": null,
"aa_start": 328,
"aa_end": null,
"aa_length": 1102,
"cds_start": 984,
"cds_end": null,
"cds_length": 3309,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001841.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "FMN2",
"gene_hgnc_id": 14074,
"hgvs_c": "c.1986+19394_1986+19426delACCCGGAGCGGCAATACCCCCTCCGCCCCCTCT",
"hgvs_p": null,
"transcript": "NM_001348094.2",
"protein_id": "NP_001335023.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 998,
"cds_start": null,
"cds_end": null,
"cds_length": 2997,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001348094.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "FMN2",
"gene_hgnc_id": 14074,
"hgvs_c": "c.188+664_188+696delACCCGGAGCGGCAATACCCCCTCCGCCCCCTCT",
"hgvs_p": null,
"transcript": "ENST00000679980.1",
"protein_id": "ENSP00000505449.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 478,
"cds_start": null,
"cds_end": null,
"cds_length": 1437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000679980.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "FMN2",
"gene_hgnc_id": 14074,
"hgvs_c": "c.285+19394_285+19426delACCCGGAGCGGCAATACCCCCTCCGCCCCCTCT",
"hgvs_p": null,
"transcript": "ENST00000681210.1",
"protein_id": "ENSP00000505131.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 462,
"cds_start": null,
"cds_end": null,
"cds_length": 1389,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000681210.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "FMN2",
"gene_hgnc_id": 14074,
"hgvs_c": "c.285+19394_285+19426delACCCGGAGCGGCAATACCCCCTCCGCCCCCTCT",
"hgvs_p": null,
"transcript": "ENST00000681824.1",
"protein_id": "ENSP00000505818.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 431,
"cds_start": null,
"cds_end": null,
"cds_length": 1296,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000681824.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "FMN2",
"gene_hgnc_id": 14074,
"hgvs_c": "c.54+19394_54+19426delACCCGGAGCGGCAATACCCCCTCCGCCCCCTCT",
"hgvs_p": null,
"transcript": "ENST00000545751.3",
"protein_id": "ENSP00000437918.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 335,
"cds_start": null,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000545751.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "FMN2",
"gene_hgnc_id": 14074,
"hgvs_c": "n.286-3435_286-3403delACCCGGAGCGGCAATACCCCCTCCGCCCCCTCT",
"hgvs_p": null,
"transcript": "ENST00000681741.1",
"protein_id": "ENSP00000505116.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000681741.1"
}
],
"gene_symbol": "FMN2",
"gene_hgnc_id": 14074,
"dbsnp": "rs758726356",
"frequency_reference_population": 0.007737864,
"hom_count_reference_population": 0,
"allele_count_reference_population": 358,
"gnomad_exomes_af": 0.00445085,
"gnomad_genomes_af": 0.00773786,
"gnomad_exomes_ac": 3844,
"gnomad_genomes_ac": 358,
"gnomad_exomes_homalt": 32,
"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": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 2.821,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -10,
"acmg_classification": "Benign",
"acmg_criteria": "PM4,BP6_Very_Strong,BS1",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 12,
"pathogenic_score": 2,
"criteria": [
"PM4",
"BP6_Very_Strong",
"BS1"
],
"verdict": "Benign",
"transcript": "NM_001305424.2",
"gene_symbol": "FMN2",
"hgnc_id": 14074,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2856_2888delACCCGGAGCGGCAATACCCCCTCCGCCCCCTCT",
"hgvs_p": "p.Pro953_Leu963del"
}
],
"clinvar_disease": " autosomal recessive 47,Intellectual disability,not provided,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4",
"phenotype_combined": "not provided|not specified|Intellectual disability, autosomal recessive 47",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}