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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: 19-35126873-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=35126873&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 35126873,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_139284.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "c.773G>A",
"hgvs_p": "p.Arg258Gln",
"transcript": "NM_139284.3",
"protein_id": "NP_644813.1",
"transcript_support_level": null,
"aa_start": 258,
"aa_end": null,
"aa_length": 537,
"cds_start": 773,
"cds_end": null,
"cds_length": 1614,
"cdna_start": 1152,
"cdna_end": null,
"cdna_length": 2673,
"mane_select": "ENST00000310123.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "c.773G>A",
"hgvs_p": "p.Arg258Gln",
"transcript": "ENST00000310123.8",
"protein_id": "ENSP00000312273.3",
"transcript_support_level": 1,
"aa_start": 258,
"aa_end": null,
"aa_length": 537,
"cds_start": 773,
"cds_end": null,
"cds_length": 1614,
"cdna_start": 1152,
"cdna_end": null,
"cdna_length": 2673,
"mane_select": "NM_139284.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "c.506G>A",
"hgvs_p": "p.Arg169Gln",
"transcript": "ENST00000587780.5",
"protein_id": "ENSP00000467044.2",
"transcript_support_level": 1,
"aa_start": 169,
"aa_end": null,
"aa_length": 377,
"cds_start": 506,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 508,
"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": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "n.832G>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": "R",
"aa_alt": "Q",
"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.773G>A",
"hgvs_p": "p.Arg258Gln",
"transcript": "ENST00000392225.7",
"protein_id": "ENSP00000376059.3",
"transcript_support_level": 5,
"aa_start": 258,
"aa_end": null,
"aa_length": 494,
"cds_start": 773,
"cds_end": null,
"cds_length": 1485,
"cdna_start": 1293,
"cdna_end": null,
"cdna_length": 2891,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "c.257G>A",
"hgvs_p": "p.Arg86Gln",
"transcript": "XM_017026428.1",
"protein_id": "XP_016881917.1",
"transcript_support_level": null,
"aa_start": 86,
"aa_end": null,
"aa_length": 365,
"cds_start": 257,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 696,
"cdna_end": null,
"cdna_length": 2217,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "c.257G>A",
"hgvs_p": "p.Arg86Gln",
"transcript": "XM_017026429.1",
"protein_id": "XP_016881918.1",
"transcript_support_level": null,
"aa_start": 86,
"aa_end": null,
"aa_length": 365,
"cds_start": 257,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 768,
"cdna_end": null,
"cdna_length": 2289,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "c.257G>A",
"hgvs_p": "p.Arg86Gln",
"transcript": "XM_017026430.2",
"protein_id": "XP_016881919.1",
"transcript_support_level": null,
"aa_start": 86,
"aa_end": null,
"aa_length": 365,
"cds_start": 257,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 549,
"cdna_end": null,
"cdna_length": 2070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LGI4",
"gene_hgnc_id": 18712,
"hgvs_c": "c.257G>A",
"hgvs_p": "p.Arg86Gln",
"transcript": "XM_047438343.1",
"protein_id": "XP_047294299.1",
"transcript_support_level": null,
"aa_start": 86,
"aa_end": null,
"aa_length": 365,
"cds_start": 257,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 823,
"cdna_end": null,
"cdna_length": 2344,
"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.904G>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.420-2007G>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": "rs755500591",
"frequency_reference_population": 0.0000037213827,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000273952,
"gnomad_genomes_af": 0.0000131411,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11770060658454895,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.066,
"revel_prediction": "Benign",
"alphamissense_score": 0.0702,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.42,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.341,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PM5,BP4_Moderate",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 2,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PM5",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_139284.3",
"gene_symbol": "LGI4",
"hgnc_id": 18712,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.773G>A",
"hgvs_p": "p.Arg258Gln"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}