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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: 1-248812238-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=248812238&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 248812238,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_030645.3",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5L",
"gene_hgnc_id": 29360,
"hgvs_c": "c.844C>T",
"hgvs_p": "p.His282Tyr",
"transcript": "NM_030645.3",
"protein_id": "NP_085148.1",
"transcript_support_level": null,
"aa_start": 282,
"aa_end": null,
"aa_length": 393,
"cds_start": 844,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 1356,
"cdna_end": null,
"cdna_length": 3148,
"mane_select": "ENST00000366472.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5L",
"gene_hgnc_id": 29360,
"hgvs_c": "c.844C>T",
"hgvs_p": "p.His282Tyr",
"transcript": "ENST00000366472.6",
"protein_id": "ENSP00000355428.5",
"transcript_support_level": 1,
"aa_start": 282,
"aa_end": null,
"aa_length": 393,
"cds_start": 844,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 1356,
"cdna_end": null,
"cdna_length": 3148,
"mane_select": "NM_030645.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5L",
"gene_hgnc_id": 29360,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.His163Tyr",
"transcript": "NM_001322462.1",
"protein_id": "NP_001309391.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 274,
"cds_start": 487,
"cds_end": null,
"cds_length": 825,
"cdna_start": 2067,
"cdna_end": null,
"cdna_length": 3859,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5L",
"gene_hgnc_id": 29360,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.His163Tyr",
"transcript": "NM_001322463.1",
"protein_id": "NP_001309392.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 274,
"cds_start": 487,
"cds_end": null,
"cds_length": 825,
"cdna_start": 1442,
"cdna_end": null,
"cdna_length": 3234,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5L",
"gene_hgnc_id": 29360,
"hgvs_c": "c.343C>T",
"hgvs_p": "p.His115Tyr",
"transcript": "NM_001322464.2",
"protein_id": "NP_001309393.1",
"transcript_support_level": null,
"aa_start": 115,
"aa_end": null,
"aa_length": 226,
"cds_start": 343,
"cds_end": null,
"cds_length": 681,
"cdna_start": 1439,
"cdna_end": null,
"cdna_length": 3231,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5L",
"gene_hgnc_id": 29360,
"hgvs_c": "c.418C>T",
"hgvs_p": "p.His140Tyr",
"transcript": "XM_047431089.1",
"protein_id": "XP_047287045.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 251,
"cds_start": 418,
"cds_end": null,
"cds_length": 756,
"cdna_start": 1589,
"cdna_end": null,
"cdna_length": 3381,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5L",
"gene_hgnc_id": 29360,
"hgvs_c": "c.418C>T",
"hgvs_p": "p.His140Tyr",
"transcript": "XM_047431099.1",
"protein_id": "XP_047287055.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 251,
"cds_start": 418,
"cds_end": null,
"cds_length": 756,
"cdna_start": 1286,
"cdna_end": null,
"cdna_length": 3078,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5L",
"gene_hgnc_id": 29360,
"hgvs_c": "c.418C>T",
"hgvs_p": "p.His140Tyr",
"transcript": "XM_047431109.1",
"protein_id": "XP_047287065.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 251,
"cds_start": 418,
"cds_end": null,
"cds_length": 756,
"cdna_start": 1602,
"cdna_end": null,
"cdna_length": 3394,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5L",
"gene_hgnc_id": 29360,
"hgvs_c": "n.2336C>T",
"hgvs_p": null,
"transcript": "ENST00000475978.1",
"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": 4122,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3BP5L",
"gene_hgnc_id": 29360,
"hgvs_c": "n.1318C>T",
"hgvs_p": null,
"transcript": "ENST00000484202.2",
"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": 3110,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SH3BP5L",
"gene_hgnc_id": 29360,
"dbsnp": "rs769626318",
"frequency_reference_population": 0.000008697748,
"hom_count_reference_population": 0,
"allele_count_reference_population": 14,
"gnomad_exomes_af": 0.00000891971,
"gnomad_genomes_af": 0.00000657177,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08418822288513184,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.104,
"revel_prediction": "Benign",
"alphamissense_score": 0.087,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.31,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_030645.3",
"gene_symbol": "SH3BP5L",
"hgnc_id": 29360,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.844C>T",
"hgvs_p": "p.His282Tyr"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}