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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: 15-64963704-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=64963704&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 64963704,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000204566.7",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPG21",
"gene_hgnc_id": 20373,
"hgvs_c": "c.843C>T",
"hgvs_p": "p.Tyr281Tyr",
"transcript": "NM_016630.7",
"protein_id": "NP_057714.1",
"transcript_support_level": null,
"aa_start": 281,
"aa_end": null,
"aa_length": 308,
"cds_start": 843,
"cds_end": null,
"cds_length": 927,
"cdna_start": 1117,
"cdna_end": null,
"cdna_length": 1799,
"mane_select": "ENST00000204566.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPG21",
"gene_hgnc_id": 20373,
"hgvs_c": "c.843C>T",
"hgvs_p": "p.Tyr281Tyr",
"transcript": "ENST00000204566.7",
"protein_id": "ENSP00000204566.2",
"transcript_support_level": 1,
"aa_start": 281,
"aa_end": null,
"aa_length": 308,
"cds_start": 843,
"cds_end": null,
"cds_length": 927,
"cdna_start": 1117,
"cdna_end": null,
"cdna_length": 1799,
"mane_select": "NM_016630.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPG21",
"gene_hgnc_id": 20373,
"hgvs_c": "c.843C>T",
"hgvs_p": "p.Tyr281Tyr",
"transcript": "ENST00000433215.6",
"protein_id": "ENSP00000404111.2",
"transcript_support_level": 1,
"aa_start": 281,
"aa_end": null,
"aa_length": 308,
"cds_start": 843,
"cds_end": null,
"cds_length": 927,
"cdna_start": 936,
"cdna_end": null,
"cdna_length": 1613,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPG21",
"gene_hgnc_id": 20373,
"hgvs_c": "c.843C>T",
"hgvs_p": "p.Tyr281Tyr",
"transcript": "NM_001127889.5",
"protein_id": "NP_001121361.1",
"transcript_support_level": null,
"aa_start": 281,
"aa_end": null,
"aa_length": 308,
"cds_start": 843,
"cds_end": null,
"cds_length": 927,
"cdna_start": 932,
"cdna_end": null,
"cdna_length": 1614,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPG21",
"gene_hgnc_id": 20373,
"hgvs_c": "c.762C>T",
"hgvs_p": "p.Tyr254Tyr",
"transcript": "NM_001127890.5",
"protein_id": "NP_001121362.1",
"transcript_support_level": null,
"aa_start": 254,
"aa_end": null,
"aa_length": 281,
"cds_start": 762,
"cds_end": null,
"cds_length": 846,
"cdna_start": 1036,
"cdna_end": null,
"cdna_length": 1718,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPG21",
"gene_hgnc_id": 20373,
"hgvs_c": "c.762C>T",
"hgvs_p": "p.Tyr254Tyr",
"transcript": "ENST00000416889.6",
"protein_id": "ENSP00000394846.2",
"transcript_support_level": 2,
"aa_start": 254,
"aa_end": null,
"aa_length": 281,
"cds_start": 762,
"cds_end": null,
"cds_length": 846,
"cdna_start": 1033,
"cdna_end": null,
"cdna_length": 1533,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPG21",
"gene_hgnc_id": 20373,
"hgvs_c": "c.381C>T",
"hgvs_p": "p.Tyr127Tyr",
"transcript": "ENST00000559199.5",
"protein_id": "ENSP00000456365.1",
"transcript_support_level": 2,
"aa_start": 127,
"aa_end": null,
"aa_length": 154,
"cds_start": 381,
"cds_end": null,
"cds_length": 465,
"cdna_start": 1382,
"cdna_end": null,
"cdna_length": 2059,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPG21",
"gene_hgnc_id": 20373,
"hgvs_c": "n.*307C>T",
"hgvs_p": null,
"transcript": "ENST00000561078.5",
"protein_id": "ENSP00000452865.1",
"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": 1520,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPG21",
"gene_hgnc_id": 20373,
"hgvs_c": "n.*307C>T",
"hgvs_p": null,
"transcript": "ENST00000561078.5",
"protein_id": "ENSP00000452865.1",
"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": 1520,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SPG21",
"gene_hgnc_id": 20373,
"dbsnp": "rs147428832",
"frequency_reference_population": 0.019601308,
"hom_count_reference_population": 383,
"allele_count_reference_population": 31636,
"gnomad_exomes_af": 0.0202057,
"gnomad_genomes_af": 0.0138012,
"gnomad_exomes_ac": 29534,
"gnomad_genomes_ac": 2102,
"gnomad_exomes_homalt": 361,
"gnomad_genomes_homalt": 22,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5799999833106995,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.015,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": "ENST00000204566.7",
"gene_symbol": "SPG21",
"hgnc_id": 20373,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.843C>T",
"hgvs_p": "p.Tyr281Tyr"
}
],
"clinvar_disease": "Hereditary spastic paraplegia,Mast syndrome,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:4",
"phenotype_combined": "Mast syndrome|not specified|Hereditary spastic paraplegia|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}