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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: 12-49954663-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=49954663&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 49954663,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000199280.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AQP2",
"gene_hgnc_id": 634,
"hgvs_c": "c.559C>T",
"hgvs_p": "p.Arg187Cys",
"transcript": "NM_000486.6",
"protein_id": "NP_000477.1",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 271,
"cds_start": 559,
"cds_end": null,
"cds_length": 816,
"cdna_start": 653,
"cdna_end": null,
"cdna_length": 4180,
"mane_select": "ENST00000199280.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AQP2",
"gene_hgnc_id": 634,
"hgvs_c": "c.559C>T",
"hgvs_p": "p.Arg187Cys",
"transcript": "ENST00000199280.4",
"protein_id": "ENSP00000199280.3",
"transcript_support_level": 1,
"aa_start": 187,
"aa_end": null,
"aa_length": 271,
"cds_start": 559,
"cds_end": null,
"cds_length": 816,
"cdna_start": 653,
"cdna_end": null,
"cdna_length": 4180,
"mane_select": "NM_000486.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AQP2",
"gene_hgnc_id": 634,
"hgvs_c": "c.685C>T",
"hgvs_p": "p.Arg229Cys",
"transcript": "ENST00000550862.1",
"protein_id": "ENSP00000450022.1",
"transcript_support_level": 5,
"aa_start": 229,
"aa_end": null,
"aa_length": 243,
"cds_start": 685,
"cds_end": null,
"cds_length": 732,
"cdna_start": 762,
"cdna_end": null,
"cdna_length": 809,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AQP2",
"gene_hgnc_id": 634,
"hgvs_c": "n.559C>T",
"hgvs_p": null,
"transcript": "ENST00000551526.5",
"protein_id": "ENSP00000447148.1",
"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": 1762,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "AQP5-AS1",
"gene_hgnc_id": 55474,
"hgvs_c": "n.118-2575G>A",
"hgvs_p": null,
"transcript": "ENST00000550530.1",
"protein_id": null,
"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": 445,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "AQP5-AS1",
"gene_hgnc_id": 55474,
"hgvs_c": "n.257-315G>A",
"hgvs_p": null,
"transcript": "ENST00000552379.1",
"protein_id": null,
"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": 592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000257378",
"gene_hgnc_id": null,
"hgvs_c": "n.542-6G>A",
"hgvs_p": null,
"transcript": "ENST00000552806.1",
"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": 560,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "AQP5-AS1",
"gene_hgnc_id": 55474,
"hgvs_c": "n.257-315G>A",
"hgvs_p": null,
"transcript": "NR_110590.1",
"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": 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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "AQP5-AS1",
"gene_hgnc_id": 55474,
"hgvs_c": "n.118-2575G>A",
"hgvs_p": null,
"transcript": "NR_110591.1",
"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": 445,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AQP2",
"gene_hgnc_id": 634,
"dbsnp": "rs104894328",
"frequency_reference_population": 0.00003593356,
"hom_count_reference_population": 0,
"allele_count_reference_population": 58,
"gnomad_exomes_af": 0.0000355705,
"gnomad_genomes_af": 0.0000394208,
"gnomad_exomes_ac": 52,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.949678897857666,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.844,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9472,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.38,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.848,
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PM1",
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000199280.4",
"gene_symbol": "AQP2",
"hgnc_id": 634,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.559C>T",
"hgvs_p": "p.Arg187Cys"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000552806.1",
"gene_symbol": "ENSG00000257378",
"hgnc_id": null,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.542-6G>A",
"hgvs_p": null
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000550530.1",
"gene_symbol": "AQP5-AS1",
"hgnc_id": 55474,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.118-2575G>A",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal, nephrogenic,Diabetes insipidus,Nephrogenic diabetes insipidus,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4 LP:1",
"phenotype_combined": "Diabetes insipidus, nephrogenic, autosomal|Nephrogenic diabetes insipidus|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}