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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: 9-136674750-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=136674750&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 136674750,
"ref": "T",
"alt": "A",
"effect": "stop_gained",
"transcript": "NM_006412.4",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGPAT2",
"gene_hgnc_id": 325,
"hgvs_c": "c.646A>T",
"hgvs_p": "p.Lys216*",
"transcript": "NM_006412.4",
"protein_id": "NP_006403.2",
"transcript_support_level": null,
"aa_start": 216,
"aa_end": null,
"aa_length": 278,
"cds_start": 646,
"cds_end": null,
"cds_length": 837,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000371696.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006412.4"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGPAT2",
"gene_hgnc_id": 325,
"hgvs_c": "c.646A>T",
"hgvs_p": "p.Lys216*",
"transcript": "ENST00000371696.7",
"protein_id": "ENSP00000360761.2",
"transcript_support_level": 1,
"aa_start": 216,
"aa_end": null,
"aa_length": 278,
"cds_start": 646,
"cds_end": null,
"cds_length": 837,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006412.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371696.7"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGPAT2",
"gene_hgnc_id": 325,
"hgvs_c": "c.550A>T",
"hgvs_p": "p.Lys184*",
"transcript": "ENST00000371694.7",
"protein_id": "ENSP00000360759.3",
"transcript_support_level": 1,
"aa_start": 184,
"aa_end": null,
"aa_length": 246,
"cds_start": 550,
"cds_end": null,
"cds_length": 741,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000371694.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGPAT2",
"gene_hgnc_id": 325,
"hgvs_c": "n.574A>T",
"hgvs_p": null,
"transcript": "ENST00000472820.1",
"protein_id": null,
"transcript_support_level": 1,
"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": "retained_intron",
"feature": "ENST00000472820.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGPAT2",
"gene_hgnc_id": 325,
"hgvs_c": "c.760A>T",
"hgvs_p": "p.Lys254*",
"transcript": "ENST00000951406.1",
"protein_id": "ENSP00000621465.1",
"transcript_support_level": null,
"aa_start": 254,
"aa_end": null,
"aa_length": 316,
"cds_start": 760,
"cds_end": null,
"cds_length": 951,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951406.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGPAT2",
"gene_hgnc_id": 325,
"hgvs_c": "c.718A>T",
"hgvs_p": "p.Lys240*",
"transcript": "ENST00000951405.1",
"protein_id": "ENSP00000621464.1",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 302,
"cds_start": 718,
"cds_end": null,
"cds_length": 909,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951405.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGPAT2",
"gene_hgnc_id": 325,
"hgvs_c": "c.706A>T",
"hgvs_p": "p.Lys236*",
"transcript": "ENST00000882836.1",
"protein_id": "ENSP00000552895.1",
"transcript_support_level": null,
"aa_start": 236,
"aa_end": null,
"aa_length": 298,
"cds_start": 706,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882836.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGPAT2",
"gene_hgnc_id": 325,
"hgvs_c": "c.646A>T",
"hgvs_p": "p.Lys216*",
"transcript": "ENST00000882838.1",
"protein_id": "ENSP00000552897.1",
"transcript_support_level": null,
"aa_start": 216,
"aa_end": null,
"aa_length": 291,
"cds_start": 646,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882838.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGPAT2",
"gene_hgnc_id": 325,
"hgvs_c": "c.682A>T",
"hgvs_p": "p.Lys228*",
"transcript": "ENST00000882833.1",
"protein_id": "ENSP00000552892.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 290,
"cds_start": 682,
"cds_end": null,
"cds_length": 873,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882833.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGPAT2",
"gene_hgnc_id": 325,
"hgvs_c": "c.679A>T",
"hgvs_p": "p.Lys227*",
"transcript": "ENST00000882832.1",
"protein_id": "ENSP00000552891.1",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 289,
"cds_start": 679,
"cds_end": null,
"cds_length": 870,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882832.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGPAT2",
"gene_hgnc_id": 325,
"hgvs_c": "c.664A>T",
"hgvs_p": "p.Lys222*",
"transcript": "ENST00000882834.1",
"protein_id": "ENSP00000552893.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 284,
"cds_start": 664,
"cds_end": null,
"cds_length": 855,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882834.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGPAT2",
"gene_hgnc_id": 325,
"hgvs_c": "c.646A>T",
"hgvs_p": "p.Lys216*",
"transcript": "ENST00000882835.1",
"protein_id": "ENSP00000552894.1",
"transcript_support_level": null,
"aa_start": 216,
"aa_end": null,
"aa_length": 276,
"cds_start": 646,
"cds_end": null,
"cds_length": 831,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882835.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGPAT2",
"gene_hgnc_id": 325,
"hgvs_c": "c.634A>T",
"hgvs_p": "p.Lys212*",
"transcript": "ENST00000882837.1",
"protein_id": "ENSP00000552896.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 274,
"cds_start": 634,
"cds_end": null,
"cds_length": 825,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882837.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGPAT2",
"gene_hgnc_id": 325,
"hgvs_c": "c.583A>T",
"hgvs_p": "p.Lys195*",
"transcript": "ENST00000951407.1",
"protein_id": "ENSP00000621466.1",
"transcript_support_level": null,
"aa_start": 195,
"aa_end": null,
"aa_length": 257,
"cds_start": 583,
"cds_end": null,
"cds_length": 774,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951407.1"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGPAT2",
"gene_hgnc_id": 325,
"hgvs_c": "c.550A>T",
"hgvs_p": "p.Lys184*",
"transcript": "NM_001012727.2",
"protein_id": "NP_001012745.1",
"transcript_support_level": null,
"aa_start": 184,
"aa_end": null,
"aa_length": 246,
"cds_start": 550,
"cds_end": null,
"cds_length": 741,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001012727.2"
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGPAT2",
"gene_hgnc_id": 325,
"hgvs_c": "c.337A>T",
"hgvs_p": "p.Lys113*",
"transcript": "XM_047422636.1",
"protein_id": "XP_047278592.1",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 175,
"cds_start": 337,
"cds_end": null,
"cds_length": 528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047422636.1"
}
],
"gene_symbol": "AGPAT2",
"gene_hgnc_id": 325,
"dbsnp": "rs138994150",
"frequency_reference_population": 0.00022042615,
"hom_count_reference_population": 0,
"allele_count_reference_population": 333,
"gnomad_exomes_af": 0.000139867,
"gnomad_genomes_af": 0.000939072,
"gnomad_exomes_ac": 190,
"gnomad_genomes_ac": 143,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4399999976158142,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.44,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.263,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Strong,BS1",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 4,
"pathogenic_score": 4,
"criteria": [
"PVS1_Strong",
"BS1"
],
"verdict": "Uncertain_significance",
"transcript": "NM_006412.4",
"gene_symbol": "AGPAT2",
"hgnc_id": 325,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.646A>T",
"hgvs_p": "p.Lys216*"
}
],
"clinvar_disease": "AGPAT2-related disorder,Congenital generalized lipodystrophy type 1,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 LP:3 LB:1 O:1",
"phenotype_combined": "Congenital generalized lipodystrophy type 1|not provided|AGPAT2-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}