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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: 1-197105038-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=197105038&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 197105038,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000367409.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASPM",
"gene_hgnc_id": 19048,
"hgvs_c": "c.4213C>T",
"hgvs_p": "p.Arg1405Cys",
"transcript": "NM_018136.5",
"protein_id": "NP_060606.3",
"transcript_support_level": null,
"aa_start": 1405,
"aa_end": null,
"aa_length": 3477,
"cds_start": 4213,
"cds_end": null,
"cds_length": 10434,
"cdna_start": 4445,
"cdna_end": null,
"cdna_length": 10863,
"mane_select": "ENST00000367409.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASPM",
"gene_hgnc_id": 19048,
"hgvs_c": "c.4213C>T",
"hgvs_p": "p.Arg1405Cys",
"transcript": "ENST00000367409.9",
"protein_id": "ENSP00000356379.4",
"transcript_support_level": 1,
"aa_start": 1405,
"aa_end": null,
"aa_length": 3477,
"cds_start": 4213,
"cds_end": null,
"cds_length": 10434,
"cdna_start": 4445,
"cdna_end": null,
"cdna_length": 10863,
"mane_select": "NM_018136.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "ASPM",
"gene_hgnc_id": 19048,
"hgvs_c": "c.4066-8874C>T",
"hgvs_p": null,
"transcript": "ENST00000294732.11",
"protein_id": "ENSP00000294732.7",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1892,
"cds_start": -4,
"cds_end": null,
"cds_length": 5679,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6132,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 18,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ASPM",
"gene_hgnc_id": 19048,
"hgvs_c": "n.2108-8874C>T",
"hgvs_p": null,
"transcript": "ENST00000367408.6",
"protein_id": null,
"transcript_support_level": 1,
"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": 3924,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASPM",
"gene_hgnc_id": 19048,
"hgvs_c": "c.4213C>T",
"hgvs_p": "p.Arg1405Cys",
"transcript": "ENST00000680265.1",
"protein_id": "ENSP00000505384.1",
"transcript_support_level": null,
"aa_start": 1405,
"aa_end": null,
"aa_length": 3551,
"cds_start": 4213,
"cds_end": null,
"cds_length": 10656,
"cdna_start": 4445,
"cdna_end": null,
"cdna_length": 11085,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASPM",
"gene_hgnc_id": 19048,
"hgvs_c": "c.4213C>T",
"hgvs_p": "p.Arg1405Cys",
"transcript": "ENST00000680710.1",
"protein_id": "ENSP00000506676.1",
"transcript_support_level": null,
"aa_start": 1405,
"aa_end": null,
"aa_length": 3469,
"cds_start": 4213,
"cds_end": null,
"cds_length": 10410,
"cdna_start": 4213,
"cdna_end": null,
"cdna_length": 10410,
"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": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASPM",
"gene_hgnc_id": 19048,
"hgvs_c": "n.*358C>T",
"hgvs_p": null,
"transcript": "ENST00000681879.1",
"protein_id": "ENSP00000505363.1",
"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": 4581,
"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": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASPM",
"gene_hgnc_id": 19048,
"hgvs_c": "n.*358C>T",
"hgvs_p": null,
"transcript": "ENST00000681879.1",
"protein_id": "ENSP00000505363.1",
"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": 4581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "ASPM",
"gene_hgnc_id": 19048,
"hgvs_c": "c.4066-8874C>T",
"hgvs_p": null,
"transcript": "NM_001206846.2",
"protein_id": "NP_001193775.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1892,
"cds_start": -4,
"cds_end": null,
"cds_length": 5679,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6108,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000300054",
"gene_hgnc_id": null,
"hgvs_c": "n.211-112G>A",
"hgvs_p": null,
"transcript": "ENST00000768463.1",
"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": 368,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ASPM",
"gene_hgnc_id": 19048,
"dbsnp": "rs139367209",
"frequency_reference_population": 0.0055636363,
"hom_count_reference_population": 59,
"allele_count_reference_population": 8958,
"gnomad_exomes_af": 0.00569874,
"gnomad_genomes_af": 0.00426653,
"gnomad_exomes_ac": 8310,
"gnomad_genomes_ac": 648,
"gnomad_exomes_homalt": 52,
"gnomad_genomes_homalt": 7,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.013116419315338135,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.795,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1632,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.3,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.479,
"phylop100way_prediction": "Uncertain_significance",
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "PP3,BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 20,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000367409.9",
"gene_symbol": "ASPM",
"hgnc_id": 19048,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4213C>T",
"hgvs_p": "p.Arg1405Cys"
},
{
"score": -15,
"benign_score": 16,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000768463.1",
"gene_symbol": "ENSG00000300054",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.211-112G>A",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive, primary,ASPM-related disorder,Microcephaly 5,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:5 B:6",
"phenotype_combined": "not specified|Microcephaly 5, primary, autosomal recessive|not provided|ASPM-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}