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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: 4-123056388-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=123056388&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 123056388,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000274008.5",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.2081G>A",
"hgvs_p": "p.Gly694Glu",
"transcript": "NM_145207.3",
"protein_id": "NP_660208.2",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 893,
"cds_start": 2081,
"cds_end": null,
"cds_length": 2682,
"cdna_start": 2146,
"cdna_end": null,
"cdna_length": 8116,
"mane_select": "ENST00000274008.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.2081G>A",
"hgvs_p": "p.Gly694Glu",
"transcript": "ENST00000274008.5",
"protein_id": "ENSP00000274008.3",
"transcript_support_level": 1,
"aa_start": 694,
"aa_end": null,
"aa_length": 893,
"cds_start": 2081,
"cds_end": null,
"cds_length": 2682,
"cdna_start": 2146,
"cdna_end": null,
"cdna_length": 8116,
"mane_select": "NM_145207.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "n.2123G>A",
"hgvs_p": null,
"transcript": "ENST00000422835.2",
"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": 2492,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.2153G>A",
"hgvs_p": "p.Gly718Glu",
"transcript": "NM_001438322.1",
"protein_id": "NP_001425251.1",
"transcript_support_level": null,
"aa_start": 718,
"aa_end": null,
"aa_length": 917,
"cds_start": 2153,
"cds_end": null,
"cds_length": 2754,
"cdna_start": 2218,
"cdna_end": null,
"cdna_length": 8188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.2150G>A",
"hgvs_p": "p.Gly717Glu",
"transcript": "NM_001437913.1",
"protein_id": "NP_001424842.1",
"transcript_support_level": null,
"aa_start": 717,
"aa_end": null,
"aa_length": 916,
"cds_start": 2150,
"cds_end": null,
"cds_length": 2751,
"cdna_start": 2215,
"cdna_end": null,
"cdna_length": 8185,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.2150G>A",
"hgvs_p": "p.Gly717Glu",
"transcript": "ENST00000675612.1",
"protein_id": "ENSP00000502453.1",
"transcript_support_level": null,
"aa_start": 717,
"aa_end": null,
"aa_length": 916,
"cds_start": 2150,
"cds_end": null,
"cds_length": 2751,
"cdna_start": 2223,
"cdna_end": null,
"cdna_length": 3414,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.2078G>A",
"hgvs_p": "p.Gly693Glu",
"transcript": "NM_001345856.2",
"protein_id": "NP_001332785.1",
"transcript_support_level": null,
"aa_start": 693,
"aa_end": null,
"aa_length": 892,
"cds_start": 2078,
"cds_end": null,
"cds_length": 2679,
"cdna_start": 2143,
"cdna_end": null,
"cdna_length": 8113,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.2081G>A",
"hgvs_p": "p.Gly694Glu",
"transcript": "XM_047449690.1",
"protein_id": "XP_047305646.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 835,
"cds_start": 2081,
"cds_end": null,
"cds_length": 2508,
"cdna_start": 2146,
"cdna_end": null,
"cdna_length": 2741,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.2078G>A",
"hgvs_p": "p.Gly693Glu",
"transcript": "XM_047449691.1",
"protein_id": "XP_047305647.1",
"transcript_support_level": null,
"aa_start": 693,
"aa_end": null,
"aa_length": 834,
"cds_start": 2078,
"cds_end": null,
"cds_length": 2505,
"cdna_start": 2143,
"cdna_end": null,
"cdna_length": 2738,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.2153G>A",
"hgvs_p": "p.Gly718Glu",
"transcript": "XM_017007827.3",
"protein_id": "XP_016863316.1",
"transcript_support_level": null,
"aa_start": 718,
"aa_end": null,
"aa_length": 823,
"cds_start": 2153,
"cds_end": null,
"cds_length": 2472,
"cdna_start": 2218,
"cdna_end": null,
"cdna_length": 9813,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.2153G>A",
"hgvs_p": "p.Gly718Glu",
"transcript": "XM_047449692.1",
"protein_id": "XP_047305648.1",
"transcript_support_level": null,
"aa_start": 718,
"aa_end": null,
"aa_length": 814,
"cds_start": 2153,
"cds_end": null,
"cds_length": 2445,
"cdna_start": 2218,
"cdna_end": null,
"cdna_length": 2899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.2081G>A",
"hgvs_p": "p.Gly694Glu",
"transcript": "XM_047449693.1",
"protein_id": "XP_047305649.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 799,
"cds_start": 2081,
"cds_end": null,
"cds_length": 2400,
"cdna_start": 2146,
"cdna_end": null,
"cdna_length": 9741,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.2078G>A",
"hgvs_p": "p.Gly693Glu",
"transcript": "XM_047449694.1",
"protein_id": "XP_047305650.1",
"transcript_support_level": null,
"aa_start": 693,
"aa_end": null,
"aa_length": 798,
"cds_start": 2078,
"cds_end": null,
"cds_length": 2397,
"cdna_start": 2143,
"cdna_end": null,
"cdna_length": 9738,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.2081G>A",
"hgvs_p": "p.Gly694Glu",
"transcript": "XM_047449695.1",
"protein_id": "XP_047305651.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 796,
"cds_start": 2081,
"cds_end": null,
"cds_length": 2391,
"cdna_start": 2146,
"cdna_end": null,
"cdna_length": 5676,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.2078G>A",
"hgvs_p": "p.Gly693Glu",
"transcript": "XM_047449696.1",
"protein_id": "XP_047305652.1",
"transcript_support_level": null,
"aa_start": 693,
"aa_end": null,
"aa_length": 793,
"cds_start": 2078,
"cds_end": null,
"cds_length": 2382,
"cdna_start": 2143,
"cdna_end": null,
"cdna_length": 2497,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.2081G>A",
"hgvs_p": "p.Gly694Glu",
"transcript": "XM_011531679.4",
"protein_id": "XP_011529981.1",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 790,
"cds_start": 2081,
"cds_end": null,
"cds_length": 2373,
"cdna_start": 2146,
"cdna_end": null,
"cdna_length": 2827,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.2078G>A",
"hgvs_p": "p.Gly693Glu",
"transcript": "XM_047449697.1",
"protein_id": "XP_047305653.1",
"transcript_support_level": null,
"aa_start": 693,
"aa_end": null,
"aa_length": 789,
"cds_start": 2078,
"cds_end": null,
"cds_length": 2370,
"cdna_start": 2143,
"cdna_end": null,
"cdna_length": 2824,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "c.1697G>A",
"hgvs_p": "p.Gly566Glu",
"transcript": "XM_017007829.2",
"protein_id": "XP_016863318.1",
"transcript_support_level": null,
"aa_start": 566,
"aa_end": null,
"aa_length": 765,
"cds_start": 1697,
"cds_end": null,
"cds_length": 2298,
"cdna_start": 2848,
"cdna_end": null,
"cdna_length": 8818,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 13,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "n.2144+27993G>A",
"hgvs_p": null,
"transcript": "XR_007096375.1",
"protein_id": null,
"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": 9607,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 13,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"hgvs_c": "n.2141+27993G>A",
"hgvs_p": null,
"transcript": "XR_007096376.1",
"protein_id": null,
"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": 9604,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AFG2A",
"gene_hgnc_id": 18119,
"dbsnp": "rs141576468",
"frequency_reference_population": 0.00019176847,
"hom_count_reference_population": 0,
"allele_count_reference_population": 309,
"gnomad_exomes_af": 0.000199417,
"gnomad_genomes_af": 0.000118373,
"gnomad_exomes_ac": 291,
"gnomad_genomes_ac": 18,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9629702568054199,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.8579999804496765,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.963,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9136,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.52,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.987,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.97906862200926,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP2,PP3,PP5",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PP2",
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000274008.5",
"gene_symbol": "AFG2A",
"hgnc_id": 18119,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2081G>A",
"hgvs_p": "p.Gly694Glu"
}
],
"clinvar_disease": "Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:2 US:2",
"phenotype_combined": "not provided|Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}