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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: 17-17803843-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=17803843&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 17803843,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000353383.6",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAI1",
"gene_hgnc_id": 9834,
"hgvs_c": "c.5653G>A",
"hgvs_p": "p.Asp1885Asn",
"transcript": "NM_030665.4",
"protein_id": "NP_109590.3",
"transcript_support_level": null,
"aa_start": 1885,
"aa_end": null,
"aa_length": 1906,
"cds_start": 5653,
"cds_end": null,
"cds_length": 5721,
"cdna_start": 6137,
"cdna_end": null,
"cdna_length": 7677,
"mane_select": "ENST00000353383.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAI1",
"gene_hgnc_id": 9834,
"hgvs_c": "c.5653G>A",
"hgvs_p": "p.Asp1885Asn",
"transcript": "ENST00000353383.6",
"protein_id": "ENSP00000323074.4",
"transcript_support_level": 1,
"aa_start": 1885,
"aa_end": null,
"aa_length": 1906,
"cds_start": 5653,
"cds_end": null,
"cds_length": 5721,
"cdna_start": 6137,
"cdna_end": null,
"cdna_length": 7677,
"mane_select": "NM_030665.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"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": "RAI1",
"gene_hgnc_id": 9834,
"hgvs_c": "c.217G>A",
"hgvs_p": "p.Asp73Asn",
"transcript": "ENST00000583166.1",
"protein_id": "ENSP00000463984.1",
"transcript_support_level": 2,
"aa_start": 73,
"aa_end": null,
"aa_length": 155,
"cds_start": 217,
"cds_end": null,
"cds_length": 468,
"cdna_start": 218,
"cdna_end": null,
"cdna_length": 489,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAI1",
"gene_hgnc_id": 9834,
"hgvs_c": "c.5653G>A",
"hgvs_p": "p.Asp1885Asn",
"transcript": "XM_017024027.2",
"protein_id": "XP_016879516.2",
"transcript_support_level": null,
"aa_start": 1885,
"aa_end": null,
"aa_length": 1906,
"cds_start": 5653,
"cds_end": null,
"cds_length": 5721,
"cdna_start": 5871,
"cdna_end": null,
"cdna_length": 7411,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAI1",
"gene_hgnc_id": 9834,
"hgvs_c": "c.5653G>A",
"hgvs_p": "p.Asp1885Asn",
"transcript": "XM_017024028.3",
"protein_id": "XP_016879517.2",
"transcript_support_level": null,
"aa_start": 1885,
"aa_end": null,
"aa_length": 1906,
"cds_start": 5653,
"cds_end": null,
"cds_length": 5721,
"cdna_start": 5809,
"cdna_end": null,
"cdna_length": 7349,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAI1",
"gene_hgnc_id": 9834,
"hgvs_c": "c.5653G>A",
"hgvs_p": "p.Asp1885Asn",
"transcript": "XM_047435149.1",
"protein_id": "XP_047291105.1",
"transcript_support_level": null,
"aa_start": 1885,
"aa_end": null,
"aa_length": 1906,
"cds_start": 5653,
"cds_end": null,
"cds_length": 5721,
"cdna_start": 6298,
"cdna_end": null,
"cdna_length": 7838,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAI1",
"gene_hgnc_id": 9834,
"hgvs_c": "c.5653G>A",
"hgvs_p": "p.Asp1885Asn",
"transcript": "XM_047435150.1",
"protein_id": "XP_047291106.1",
"transcript_support_level": null,
"aa_start": 1885,
"aa_end": null,
"aa_length": 1906,
"cds_start": 5653,
"cds_end": null,
"cds_length": 5721,
"cdna_start": 5771,
"cdna_end": null,
"cdna_length": 7311,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAI1",
"gene_hgnc_id": 9834,
"hgvs_c": "c.5653G>A",
"hgvs_p": "p.Asp1885Asn",
"transcript": "XM_047435151.1",
"protein_id": "XP_047291107.1",
"transcript_support_level": null,
"aa_start": 1885,
"aa_end": null,
"aa_length": 1906,
"cds_start": 5653,
"cds_end": null,
"cds_length": 5721,
"cdna_start": 8419,
"cdna_end": null,
"cdna_length": 9959,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAI1",
"gene_hgnc_id": 9834,
"hgvs_c": "c.5653G>A",
"hgvs_p": "p.Asp1885Asn",
"transcript": "XM_047435152.1",
"protein_id": "XP_047291108.1",
"transcript_support_level": null,
"aa_start": 1885,
"aa_end": null,
"aa_length": 1906,
"cds_start": 5653,
"cds_end": null,
"cds_length": 5721,
"cdna_start": 6295,
"cdna_end": null,
"cdna_length": 7835,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAI1",
"gene_hgnc_id": 9834,
"hgvs_c": "c.5653G>A",
"hgvs_p": "p.Asp1885Asn",
"transcript": "XM_047435153.1",
"protein_id": "XP_047291109.1",
"transcript_support_level": null,
"aa_start": 1885,
"aa_end": null,
"aa_length": 1906,
"cds_start": 5653,
"cds_end": null,
"cds_length": 5721,
"cdna_start": 6005,
"cdna_end": null,
"cdna_length": 7545,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RAI1",
"gene_hgnc_id": 9834,
"dbsnp": "rs147844401",
"frequency_reference_population": 0.00015745474,
"hom_count_reference_population": 0,
"allele_count_reference_population": 254,
"gnomad_exomes_af": 0.000158802,
"gnomad_genomes_af": 0.000144524,
"gnomad_exomes_ac": 232,
"gnomad_genomes_ac": 22,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.45988836884498596,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.276,
"revel_prediction": "Benign",
"alphamissense_score": 0.1183,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.753,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000353383.6",
"gene_symbol": "RAI1",
"hgnc_id": 9834,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.5653G>A",
"hgvs_p": "p.Asp1885Asn"
}
],
"clinvar_disease": "Inborn genetic diseases,RAI1-related disorder,Smith-Magenis syndrome,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1 B:2",
"phenotype_combined": "not specified|Smith-Magenis syndrome|not provided|Inborn genetic diseases|RAI1-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}