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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: 9-100284515-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=100284515&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 100284515,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "ENST00000262457.7",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INVS",
"gene_hgnc_id": 17870,
"hgvs_c": "c.1980A>G",
"hgvs_p": "p.Gly660Gly",
"transcript": "NM_014425.5",
"protein_id": "NP_055240.2",
"transcript_support_level": null,
"aa_start": 660,
"aa_end": null,
"aa_length": 1065,
"cds_start": 1980,
"cds_end": null,
"cds_length": 3198,
"cdna_start": 2178,
"cdna_end": null,
"cdna_length": 4897,
"mane_select": "ENST00000262457.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INVS",
"gene_hgnc_id": 17870,
"hgvs_c": "c.1980A>G",
"hgvs_p": "p.Gly660Gly",
"transcript": "ENST00000262457.7",
"protein_id": "ENSP00000262457.2",
"transcript_support_level": 1,
"aa_start": 660,
"aa_end": null,
"aa_length": 1065,
"cds_start": 1980,
"cds_end": null,
"cds_length": 3198,
"cdna_start": 2178,
"cdna_end": null,
"cdna_length": 4897,
"mane_select": "NM_014425.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INVS",
"gene_hgnc_id": 17870,
"hgvs_c": "c.1692A>G",
"hgvs_p": "p.Gly564Gly",
"transcript": "NM_001318381.2",
"protein_id": "NP_001305310.1",
"transcript_support_level": null,
"aa_start": 564,
"aa_end": null,
"aa_length": 969,
"cds_start": 1692,
"cds_end": null,
"cds_length": 2910,
"cdna_start": 2266,
"cdna_end": null,
"cdna_length": 4985,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INVS",
"gene_hgnc_id": 17870,
"hgvs_c": "c.1980A>G",
"hgvs_p": "p.Gly660Gly",
"transcript": "ENST00000262456.6",
"protein_id": "ENSP00000262456.2",
"transcript_support_level": 5,
"aa_start": 660,
"aa_end": null,
"aa_length": 895,
"cds_start": 1980,
"cds_end": null,
"cds_length": 2688,
"cdna_start": 2146,
"cdna_end": null,
"cdna_length": 2968,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INVS",
"gene_hgnc_id": 17870,
"hgvs_c": "c.1002A>G",
"hgvs_p": "p.Gly334Gly",
"transcript": "NM_001318382.2",
"protein_id": "NP_001305311.1",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 739,
"cds_start": 1002,
"cds_end": null,
"cds_length": 2220,
"cdna_start": 2189,
"cdna_end": null,
"cdna_length": 4908,
"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": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INVS",
"gene_hgnc_id": 17870,
"hgvs_c": "n.2178A>G",
"hgvs_p": null,
"transcript": "NR_134606.2",
"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": 4848,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124902235",
"gene_hgnc_id": null,
"hgvs_c": "n.-194T>C",
"hgvs_p": null,
"transcript": "XR_007061700.1",
"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": 6816,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "INVS",
"gene_hgnc_id": 17870,
"dbsnp": "rs139314036",
"frequency_reference_population": 0.00041385344,
"hom_count_reference_population": 5,
"allele_count_reference_population": 668,
"gnomad_exomes_af": 0.000433724,
"gnomad_genomes_af": 0.000223188,
"gnomad_exomes_ac": 634,
"gnomad_genomes_ac": 34,
"gnomad_exomes_homalt": 5,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8799999952316284,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.88,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.69,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000262457.7",
"gene_symbol": "INVS",
"hgnc_id": 17870,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1980A>G",
"hgvs_p": "p.Gly660Gly"
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "XR_007061700.1",
"gene_symbol": "LOC124902235",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-194T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Nephronophthisis,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:2",
"phenotype_combined": "not specified|Nephronophthisis",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}