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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: 17-73206754-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=73206754&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 73206754,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000299886.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG1",
"gene_hgnc_id": 6545,
"hgvs_c": "c.2666G>A",
"hgvs_p": "p.Arg889Gln",
"transcript": "NM_018714.3",
"protein_id": "NP_061184.1",
"transcript_support_level": null,
"aa_start": 889,
"aa_end": null,
"aa_length": 980,
"cds_start": 2666,
"cds_end": null,
"cds_length": 2943,
"cdna_start": 2681,
"cdna_end": null,
"cdna_length": 3014,
"mane_select": "ENST00000299886.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG1",
"gene_hgnc_id": 6545,
"hgvs_c": "c.2666G>A",
"hgvs_p": "p.Arg889Gln",
"transcript": "ENST00000299886.9",
"protein_id": "ENSP00000299886.4",
"transcript_support_level": 1,
"aa_start": 889,
"aa_end": null,
"aa_length": 980,
"cds_start": 2666,
"cds_end": null,
"cds_length": 2943,
"cdna_start": 2681,
"cdna_end": null,
"cdna_length": 3014,
"mane_select": "NM_018714.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG1",
"gene_hgnc_id": 6545,
"hgvs_c": "c.2663G>A",
"hgvs_p": "p.Arg888Gln",
"transcript": "ENST00000438720.7",
"protein_id": "ENSP00000400111.3",
"transcript_support_level": 1,
"aa_start": 888,
"aa_end": null,
"aa_length": 961,
"cds_start": 2663,
"cds_end": null,
"cds_length": 2886,
"cdna_start": 2664,
"cdna_end": null,
"cdna_length": 4051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG1",
"gene_hgnc_id": 6545,
"hgvs_c": "c.221G>A",
"hgvs_p": "p.Arg74Gln",
"transcript": "ENST00000582512.5",
"protein_id": "ENSP00000463696.1",
"transcript_support_level": 2,
"aa_start": 74,
"aa_end": null,
"aa_length": 125,
"cds_start": 221,
"cds_end": null,
"cds_length": 378,
"cdna_start": 222,
"cdna_end": null,
"cdna_length": 506,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG1",
"gene_hgnc_id": 6545,
"hgvs_c": "c.149G>A",
"hgvs_p": "p.Arg50Gln",
"transcript": "ENST00000582672.1",
"protein_id": "ENSP00000463298.1",
"transcript_support_level": 3,
"aa_start": 50,
"aa_end": null,
"aa_length": 101,
"cds_start": 149,
"cds_end": null,
"cds_length": 306,
"cdna_start": 151,
"cdna_end": null,
"cdna_length": 520,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG1",
"gene_hgnc_id": 6545,
"hgvs_c": "n.372G>A",
"hgvs_p": null,
"transcript": "ENST00000577238.1",
"protein_id": null,
"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": 707,
"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": "COG1",
"gene_hgnc_id": 6545,
"hgvs_c": "n.266G>A",
"hgvs_p": null,
"transcript": "ENST00000580271.5",
"protein_id": null,
"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": 601,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COG1",
"gene_hgnc_id": 6545,
"hgvs_c": "n.14G>A",
"hgvs_p": null,
"transcript": "ENST00000582973.1",
"protein_id": "ENSP00000462709.1",
"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": 438,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COG1",
"gene_hgnc_id": 6545,
"dbsnp": "rs148773959",
"frequency_reference_population": 0.000044666067,
"hom_count_reference_population": 1,
"allele_count_reference_population": 72,
"gnomad_exomes_af": 0.0000444687,
"gnomad_genomes_af": 0.0000465859,
"gnomad_exomes_ac": 65,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6121382713317871,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.228,
"revel_prediction": "Benign",
"alphamissense_score": 0.1242,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.506,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000299886.9",
"gene_symbol": "COG1",
"hgnc_id": 6545,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2666G>A",
"hgvs_p": "p.Arg889Gln"
}
],
"clinvar_disease": "COG1 congenital disorder of glycosylation,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "COG1 congenital disorder of glycosylation|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}