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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-153905164-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153905164&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153905164,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000054.7",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "S",
"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": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "c.19A>T",
"hgvs_p": "p.Thr7Ser",
"transcript": "NM_000054.7",
"protein_id": "NP_000045.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 371,
"cds_start": 19,
"cds_end": null,
"cds_length": 1116,
"cdna_start": 290,
"cdna_end": null,
"cdna_length": 1825,
"mane_select": "ENST00000646375.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": true,
"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": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "c.19A>T",
"hgvs_p": "p.Thr7Ser",
"transcript": "ENST00000646375.2",
"protein_id": "ENSP00000496396.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 371,
"cds_start": 19,
"cds_end": null,
"cds_length": 1116,
"cdna_start": 290,
"cdna_end": null,
"cdna_length": 1825,
"mane_select": "NM_000054.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "c.19A>T",
"hgvs_p": "p.Thr7Ser",
"transcript": "ENST00000337474.5",
"protein_id": "ENSP00000338072.5",
"transcript_support_level": 1,
"aa_start": 7,
"aa_end": null,
"aa_length": 371,
"cds_start": 19,
"cds_end": null,
"cds_length": 1116,
"cdna_start": 90,
"cdna_end": null,
"cdna_length": 1622,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "c.19A>T",
"hgvs_p": "p.Thr7Ser",
"transcript": "ENST00000370049.1",
"protein_id": "ENSP00000359066.1",
"transcript_support_level": 1,
"aa_start": 7,
"aa_end": null,
"aa_length": 309,
"cds_start": 19,
"cds_end": null,
"cds_length": 930,
"cdna_start": 51,
"cdna_end": null,
"cdna_length": 1307,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "n.19A>T",
"hgvs_p": null,
"transcript": "ENST00000434679.6",
"protein_id": "ENSP00000393397.1",
"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": 1601,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000284987",
"gene_hgnc_id": null,
"hgvs_c": "n.96+3906T>A",
"hgvs_p": null,
"transcript": "ENST00000646191.1",
"protein_id": "ENSP00000493873.1",
"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": 498,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "c.19A>T",
"hgvs_p": "p.Thr7Ser",
"transcript": "ENST00000430697.1",
"protein_id": "ENSP00000393513.1",
"transcript_support_level": 5,
"aa_start": 7,
"aa_end": null,
"aa_length": 371,
"cds_start": 19,
"cds_end": null,
"cds_length": 1116,
"cdna_start": 164,
"cdna_end": null,
"cdna_length": 1261,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "c.19A>T",
"hgvs_p": "p.Thr7Ser",
"transcript": "NM_001146151.3",
"protein_id": "NP_001139623.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 309,
"cds_start": 19,
"cds_end": null,
"cds_length": 930,
"cdna_start": 249,
"cdna_end": null,
"cdna_length": 1890,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "n.459A>T",
"hgvs_p": null,
"transcript": "NR_027419.2",
"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": 1507,
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000284987",
"gene_hgnc_id": null,
"hgvs_c": "n.154+3906T>A",
"hgvs_p": null,
"transcript": "ENST00000464967.5",
"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": 593,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000284987",
"gene_hgnc_id": null,
"hgvs_c": "n.96+3906T>A",
"hgvs_p": null,
"transcript": "ENST00000642393.1",
"protein_id": "ENSP00000495119.1",
"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": 314,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AVPR2",
"gene_hgnc_id": 897,
"dbsnp": "rs5196",
"frequency_reference_population": 0.0054402854,
"hom_count_reference_population": 1967,
"allele_count_reference_population": 6582,
"gnomad_exomes_af": 0.00344528,
"gnomad_genomes_af": 0.0250273,
"gnomad_exomes_ac": 3783,
"gnomad_genomes_ac": 2799,
"gnomad_exomes_homalt": 91,
"gnomad_genomes_homalt": 81,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0018894374370574951,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.086,
"revel_prediction": "Benign",
"alphamissense_score": 0.0827,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.7,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.473,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_000054.7",
"gene_symbol": "AVPR2",
"hgnc_id": 897,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.19A>T",
"hgvs_p": "p.Thr7Ser"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000646191.1",
"gene_symbol": "ENSG00000284987",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.96+3906T>A",
"hgvs_p": null
}
],
"clinvar_disease": " X-linked, nephrogenic,AVPR2-related disorder,Diabetes insipidus,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "Diabetes insipidus, nephrogenic, X-linked|not provided|AVPR2-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}