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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: 2-99162832-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=99162832&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 99162832,
"ref": "C",
"alt": "G",
"effect": "stop_gained",
"transcript": "ENST00000651691.1",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPT1",
"gene_hgnc_id": 29569,
"hgvs_c": "c.875C>G",
"hgvs_p": "p.Ser292*",
"transcript": "NM_145199.3",
"protein_id": "NP_660200.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 373,
"cds_start": 875,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 961,
"cdna_end": null,
"cdna_length": 1266,
"mane_select": "ENST00000651691.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPT1",
"gene_hgnc_id": 29569,
"hgvs_c": "c.875C>G",
"hgvs_p": "p.Ser292*",
"transcript": "ENST00000651691.1",
"protein_id": "ENSP00000498546.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 373,
"cds_start": 875,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 961,
"cdna_end": null,
"cdna_length": 1266,
"mane_select": "NM_145199.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPT1",
"gene_hgnc_id": 29569,
"hgvs_c": "c.875C>G",
"hgvs_p": "p.Ser292*",
"transcript": "ENST00000393473.6",
"protein_id": "ENSP00000377115.2",
"transcript_support_level": 1,
"aa_start": 292,
"aa_end": null,
"aa_length": 373,
"cds_start": 875,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 1099,
"cdna_end": null,
"cdna_length": 1424,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000273155",
"gene_hgnc_id": null,
"hgvs_c": "c.-28+6406C>G",
"hgvs_p": null,
"transcript": "ENST00000410042.1",
"protein_id": "ENSP00000387111.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 131,
"cds_start": -4,
"cds_end": null,
"cds_length": 396,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 669,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000241962",
"gene_hgnc_id": null,
"hgvs_c": "n.63+12313C>G",
"hgvs_p": null,
"transcript": "ENST00000424491.5",
"protein_id": "ENSP00000390891.1",
"transcript_support_level": 2,
"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": 1947,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPT1",
"gene_hgnc_id": 29569,
"hgvs_c": "c.875C>G",
"hgvs_p": "p.Ser292*",
"transcript": "NM_001204830.2",
"protein_id": "NP_001191759.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 373,
"cds_start": 875,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 1297,
"cdna_end": null,
"cdna_length": 1602,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPT1",
"gene_hgnc_id": 29569,
"hgvs_c": "c.875C>G",
"hgvs_p": "p.Ser292*",
"transcript": "NM_015929.4",
"protein_id": "NP_057013.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 373,
"cds_start": 875,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 1087,
"cdna_end": null,
"cdna_length": 1392,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPT1",
"gene_hgnc_id": 29569,
"hgvs_c": "c.875C>G",
"hgvs_p": "p.Ser292*",
"transcript": "NM_145197.3",
"protein_id": "NP_660198.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 373,
"cds_start": 875,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 1215,
"cdna_end": null,
"cdna_length": 1520,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPT1",
"gene_hgnc_id": 29569,
"hgvs_c": "c.875C>G",
"hgvs_p": "p.Ser292*",
"transcript": "NM_145198.3",
"protein_id": "NP_660199.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 373,
"cds_start": 875,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 1203,
"cdna_end": null,
"cdna_length": 1508,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPT1",
"gene_hgnc_id": 29569,
"hgvs_c": "c.875C>G",
"hgvs_p": "p.Ser292*",
"transcript": "ENST00000393471.2",
"protein_id": "ENSP00000377114.2",
"transcript_support_level": 2,
"aa_start": 292,
"aa_end": null,
"aa_length": 373,
"cds_start": 875,
"cds_end": null,
"cds_length": 1122,
"cdna_start": 973,
"cdna_end": null,
"cdna_length": 1289,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPT1",
"gene_hgnc_id": 29569,
"hgvs_c": "n.1360C>G",
"hgvs_p": null,
"transcript": "NR_037935.2",
"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": 1665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPT1",
"gene_hgnc_id": 29569,
"hgvs_c": "n.1024C>G",
"hgvs_p": null,
"transcript": "NR_037936.2",
"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": 1329,
"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": 8,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "MITD1",
"gene_hgnc_id": 25207,
"hgvs_c": "c.*4-614G>C",
"hgvs_p": null,
"transcript": "ENST00000422537.6",
"protein_id": "ENSP00000413371.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 231,
"cds_start": -4,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "MITD1",
"gene_hgnc_id": 25207,
"hgvs_c": "n.241-1164G>C",
"hgvs_p": null,
"transcript": "ENST00000487588.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 482,
"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": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "MITD1",
"gene_hgnc_id": 25207,
"hgvs_c": "c.730-1164G>C",
"hgvs_p": null,
"transcript": "XM_011510581.4",
"protein_id": "XP_011508883.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 291,
"cds_start": -4,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 973,
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MITD1",
"gene_hgnc_id": 25207,
"hgvs_c": "c.643-1164G>C",
"hgvs_p": null,
"transcript": "XM_017003314.3",
"protein_id": "XP_016858803.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 262,
"cds_start": -4,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 886,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LIPT1",
"gene_hgnc_id": 29569,
"hgvs_c": "c.*121C>G",
"hgvs_p": null,
"transcript": "ENST00000434566.5",
"protein_id": "ENSP00000393591.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 250,
"cds_start": -4,
"cds_end": null,
"cds_length": 754,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 885,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LIPT1",
"gene_hgnc_id": 29569,
"dbsnp": "rs137891647",
"frequency_reference_population": 0.0006897364,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1113,
"gnomad_exomes_af": 0.000715062,
"gnomad_genomes_af": 0.00044664,
"gnomad_exomes_ac": 1045,
"gnomad_genomes_ac": 68,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3199999928474426,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.32,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.865,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000651691.1",
"gene_symbol": "LIPT1",
"hgnc_id": 29569,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.875C>G",
"hgvs_p": "p.Ser292*"
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000424491.5",
"gene_symbol": "ENSG00000241962",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.63+12313C>G",
"hgvs_p": null
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000410042.1",
"gene_symbol": "ENSG00000273155",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.-28+6406C>G",
"hgvs_p": null
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000487588.5",
"gene_symbol": "MITD1",
"hgnc_id": 25207,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.241-1164G>C",
"hgvs_p": null
}
],
"clinvar_disease": "Lipoyl transferase 1 deficiency,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:7 LP:3",
"phenotype_combined": "Lipoyl transferase 1 deficiency|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}