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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-153905901-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153905901&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153905901,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000054.7",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "D",
"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": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "c.395C>A",
"hgvs_p": "p.Ala132Asp",
"transcript": "NM_000054.7",
"protein_id": "NP_000045.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 371,
"cds_start": 395,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000646375.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000054.7"
},
{
"aa_ref": "A",
"aa_alt": "D",
"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": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "c.395C>A",
"hgvs_p": "p.Ala132Asp",
"transcript": "ENST00000646375.2",
"protein_id": "ENSP00000496396.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 371,
"cds_start": 395,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000054.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000646375.2"
},
{
"aa_ref": "A",
"aa_alt": "D",
"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.395C>A",
"hgvs_p": "p.Ala132Asp",
"transcript": "ENST00000337474.5",
"protein_id": "ENSP00000338072.5",
"transcript_support_level": 1,
"aa_start": 132,
"aa_end": null,
"aa_length": 371,
"cds_start": 395,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000337474.5"
},
{
"aa_ref": "A",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "c.395C>A",
"hgvs_p": "p.Ala132Asp",
"transcript": "ENST00000370049.1",
"protein_id": "ENSP00000359066.1",
"transcript_support_level": 1,
"aa_start": 132,
"aa_end": null,
"aa_length": 309,
"cds_start": 395,
"cds_end": null,
"cds_length": 930,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370049.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "n.26-118C>A",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000434679.6"
},
{
"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+3169G>T",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000646191.1"
},
{
"aa_ref": "A",
"aa_alt": "D",
"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": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "c.419C>A",
"hgvs_p": "p.Ala140Asp",
"transcript": "ENST00000881290.1",
"protein_id": "ENSP00000551349.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 379,
"cds_start": 419,
"cds_end": null,
"cds_length": 1140,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881290.1"
},
{
"aa_ref": "A",
"aa_alt": "D",
"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.395C>A",
"hgvs_p": "p.Ala132Asp",
"transcript": "ENST00000430697.1",
"protein_id": "ENSP00000393513.1",
"transcript_support_level": 5,
"aa_start": 132,
"aa_end": null,
"aa_length": 371,
"cds_start": 395,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000430697.1"
},
{
"aa_ref": "A",
"aa_alt": "D",
"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": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "c.395C>A",
"hgvs_p": "p.Ala132Asp",
"transcript": "ENST00000881289.1",
"protein_id": "ENSP00000551348.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 371,
"cds_start": 395,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881289.1"
},
{
"aa_ref": "A",
"aa_alt": "D",
"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": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "c.395C>A",
"hgvs_p": "p.Ala132Asp",
"transcript": "ENST00000881291.1",
"protein_id": "ENSP00000551350.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 371,
"cds_start": 395,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881291.1"
},
{
"aa_ref": "A",
"aa_alt": "D",
"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": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "c.395C>A",
"hgvs_p": "p.Ala132Asp",
"transcript": "NM_001146151.3",
"protein_id": "NP_001139623.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 309,
"cds_start": 395,
"cds_end": null,
"cds_length": 930,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001146151.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "c.26-622C>A",
"hgvs_p": null,
"transcript": "ENST00000960389.1",
"protein_id": "ENSP00000630448.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 76,
"cds_start": null,
"cds_end": null,
"cds_length": 231,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960389.1"
},
{
"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+3169G>T",
"hgvs_p": null,
"transcript": "ENST00000464967.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000464967.5"
},
{
"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+3169G>T",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000642393.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "AVPR2",
"gene_hgnc_id": 897,
"hgvs_c": "n.466-118C>A",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_027419.2"
}
],
"gene_symbol": "AVPR2",
"gene_hgnc_id": 897,
"dbsnp": "rs104894747",
"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": 0.9709517955780029,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.755,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9377,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.19,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.175,
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM1",
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_000054.7",
"gene_symbol": "AVPR2",
"hgnc_id": 897,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.395C>A",
"hgvs_p": "p.Ala132Asp"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000646191.1",
"gene_symbol": "ENSG00000284987",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.96+3169G>T",
"hgvs_p": null
}
],
"clinvar_disease": " X-linked, nephrogenic,Diabetes insipidus",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Diabetes insipidus, nephrogenic, X-linked",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}