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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: 19-35126706-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=35126706&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 35126706,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000310123.8",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "c.863G>A",
"hgvs_p": "p.Trp288*",
"transcript": "NM_139284.3",
"protein_id": "NP_644813.1",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 537,
"cds_start": 863,
"cds_end": null,
"cds_length": 1614,
"cdna_start": 1242,
"cdna_end": null,
"cdna_length": 2673,
"mane_select": "ENST00000310123.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "c.863G>A",
"hgvs_p": "p.Trp288*",
"transcript": "ENST00000310123.8",
"protein_id": "ENSP00000312273.3",
"transcript_support_level": 1,
"aa_start": 288,
"aa_end": null,
"aa_length": 537,
"cds_start": 863,
"cds_end": null,
"cds_length": 1614,
"cdna_start": 1242,
"cdna_end": null,
"cdna_length": 2673,
"mane_select": "NM_139284.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "c.596G>A",
"hgvs_p": "p.Trp199*",
"transcript": "ENST00000587780.5",
"protein_id": "ENSP00000467044.2",
"transcript_support_level": 1,
"aa_start": 199,
"aa_end": null,
"aa_length": 377,
"cds_start": 596,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 598,
"cdna_end": null,
"cdna_length": 2630,
"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": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "n.922G>A",
"hgvs_p": null,
"transcript": "ENST00000493050.5",
"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": 2200,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "c.347G>A",
"hgvs_p": "p.Trp116*",
"transcript": "XM_017026428.1",
"protein_id": "XP_016881917.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 365,
"cds_start": 347,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 786,
"cdna_end": null,
"cdna_length": 2217,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "c.347G>A",
"hgvs_p": "p.Trp116*",
"transcript": "XM_017026429.1",
"protein_id": "XP_016881918.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 365,
"cds_start": 347,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 858,
"cdna_end": null,
"cdna_length": 2289,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "c.347G>A",
"hgvs_p": "p.Trp116*",
"transcript": "XM_017026430.2",
"protein_id": "XP_016881919.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 365,
"cds_start": 347,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 639,
"cdna_end": null,
"cdna_length": 2070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "c.347G>A",
"hgvs_p": "p.Trp116*",
"transcript": "XM_047438343.1",
"protein_id": "XP_047294299.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 365,
"cds_start": 347,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 913,
"cdna_end": null,
"cdna_length": 2344,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "c.940G>A",
"hgvs_p": "p.Gly314Arg",
"transcript": "ENST00000392225.7",
"protein_id": "ENSP00000376059.3",
"transcript_support_level": 5,
"aa_start": 314,
"aa_end": null,
"aa_length": 494,
"cds_start": 940,
"cds_end": null,
"cds_length": 1485,
"cdna_start": 1460,
"cdna_end": null,
"cdna_length": 2891,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "n.1071G>A",
"hgvs_p": null,
"transcript": "ENST00000593248.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 1076,
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "n.420-1840G>A",
"hgvs_p": null,
"transcript": "ENST00000591840.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"dbsnp": "rs775997446",
"frequency_reference_population": 0.0000036070196,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000360702,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4776420295238495,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.26,
"revel_prediction": "Benign",
"alphamissense_score": 0.1913,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.18,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.966,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000310123.8",
"gene_symbol": "LGI4",
"hgnc_id": 18712,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.863G>A",
"hgvs_p": "p.Trp288*"
}
],
"clinvar_disease": " neurogenic, with myelin defect,Arthrogryposis multiplex congenita 1",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Arthrogryposis multiplex congenita 1, neurogenic, with myelin defect",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}