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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: X-110201042-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=110201042&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 110201042,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_015365.3",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "Y",
"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": "AMMECR1",
"gene_hgnc_id": 467,
"hgvs_c": "c.799C>T",
"hgvs_p": "p.His267Tyr",
"transcript": "NM_015365.3",
"protein_id": "NP_056180.1",
"transcript_support_level": null,
"aa_start": 267,
"aa_end": null,
"aa_length": 333,
"cds_start": 799,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 813,
"cdna_end": null,
"cdna_length": 5350,
"mane_select": "ENST00000262844.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": true,
"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": "AMMECR1",
"gene_hgnc_id": 467,
"hgvs_c": "c.799C>T",
"hgvs_p": "p.His267Tyr",
"transcript": "ENST00000262844.10",
"protein_id": "ENSP00000262844.5",
"transcript_support_level": 1,
"aa_start": 267,
"aa_end": null,
"aa_length": 333,
"cds_start": 799,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 813,
"cdna_end": null,
"cdna_length": 5350,
"mane_select": "NM_015365.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMMECR1",
"gene_hgnc_id": 467,
"hgvs_c": "c.688C>T",
"hgvs_p": "p.His230Tyr",
"transcript": "ENST00000372059.6",
"protein_id": "ENSP00000361129.2",
"transcript_support_level": 1,
"aa_start": 230,
"aa_end": null,
"aa_length": 296,
"cds_start": 688,
"cds_end": null,
"cds_length": 891,
"cdna_start": 701,
"cdna_end": null,
"cdna_length": 3052,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMMECR1",
"gene_hgnc_id": 467,
"hgvs_c": "c.799C>T",
"hgvs_p": "p.His267Tyr",
"transcript": "ENST00000686065.1",
"protein_id": "ENSP00000509935.1",
"transcript_support_level": null,
"aa_start": 267,
"aa_end": null,
"aa_length": 319,
"cds_start": 799,
"cds_end": null,
"cds_length": 960,
"cdna_start": 813,
"cdna_end": null,
"cdna_length": 5424,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMMECR1",
"gene_hgnc_id": 467,
"hgvs_c": "c.688C>T",
"hgvs_p": "p.His230Tyr",
"transcript": "NM_001025580.2",
"protein_id": "NP_001020751.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 296,
"cds_start": 688,
"cds_end": null,
"cds_length": 891,
"cdna_start": 702,
"cdna_end": null,
"cdna_length": 5239,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"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": "AMMECR1",
"gene_hgnc_id": 467,
"hgvs_c": "c.430C>T",
"hgvs_p": "p.His144Tyr",
"transcript": "NM_001171689.2",
"protein_id": "NP_001165160.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 210,
"cds_start": 430,
"cds_end": null,
"cds_length": 633,
"cdna_start": 1067,
"cdna_end": null,
"cdna_length": 5604,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"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": "AMMECR1",
"gene_hgnc_id": 467,
"hgvs_c": "c.430C>T",
"hgvs_p": "p.His144Tyr",
"transcript": "ENST00000372057.1",
"protein_id": "ENSP00000361127.1",
"transcript_support_level": 2,
"aa_start": 144,
"aa_end": null,
"aa_length": 210,
"cds_start": 430,
"cds_end": null,
"cds_length": 633,
"cdna_start": 1067,
"cdna_end": null,
"cdna_length": 3380,
"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": "AMMECR1",
"gene_hgnc_id": 467,
"hgvs_c": "n.1033C>T",
"hgvs_p": null,
"transcript": "ENST00000680410.1",
"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": 3318,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AMMECR1",
"gene_hgnc_id": 467,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.818124532699585,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.358,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9069,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.23,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.599,
"phylop100way_prediction": "Pathogenic",
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_015365.3",
"gene_symbol": "AMMECR1",
"hgnc_id": 467,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.799C>T",
"hgvs_p": "p.His267Tyr"
}
],
"clinvar_disease": " and nephrocalcinosis, elliptocytosis, hearing impairment,Midface hypoplasia",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}