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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: 9-4574022-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=4574022&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 4574022,
"ref": "A",
"alt": "C",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000262352.8",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SLC1A1",
"gene_hgnc_id": 10939,
"hgvs_c": "c.875+8A>C",
"hgvs_p": null,
"transcript": "NM_004170.6",
"protein_id": "NP_004161.4",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 524,
"cds_start": -4,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3698,
"mane_select": "ENST00000262352.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SLC1A1",
"gene_hgnc_id": 10939,
"hgvs_c": "c.875+8A>C",
"hgvs_p": null,
"transcript": "ENST00000262352.8",
"protein_id": "ENSP00000262352.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 524,
"cds_start": -4,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3698,
"mane_select": "NM_004170.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC1A1",
"gene_hgnc_id": 10939,
"hgvs_c": "c.161+8A>C",
"hgvs_p": null,
"transcript": "ENST00000422398.1",
"protein_id": "ENSP00000414620.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 240,
"cds_start": -4,
"cds_end": null,
"cds_length": 725,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 726,
"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": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "SPATA6L",
"gene_hgnc_id": 25472,
"hgvs_c": "n.*782-19634T>G",
"hgvs_p": null,
"transcript": "ENST00000485616.5",
"protein_id": "ENSP00000420003.1",
"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": 2437,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "SLC1A1",
"gene_hgnc_id": 10939,
"hgvs_c": "c.944+8A>C",
"hgvs_p": null,
"transcript": "XM_011518007.2",
"protein_id": "XP_011516309.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 547,
"cds_start": -4,
"cds_end": null,
"cds_length": 1644,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3767,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "SLC1A1",
"gene_hgnc_id": 10939,
"hgvs_c": "c.884+8A>C",
"hgvs_p": null,
"transcript": "XM_011518008.4",
"protein_id": "XP_011516310.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 527,
"cds_start": -4,
"cds_end": null,
"cds_length": 1584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3799,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SLC1A1",
"gene_hgnc_id": 10939,
"hgvs_c": "c.836+1634A>C",
"hgvs_p": null,
"transcript": "XM_017015042.2",
"protein_id": "XP_016870531.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 511,
"cds_start": -4,
"cds_end": null,
"cds_length": 1536,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3659,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SLC1A1",
"gene_hgnc_id": 10939,
"hgvs_c": "c.815+8A>C",
"hgvs_p": null,
"transcript": "XM_011518009.4",
"protein_id": "XP_011516311.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 504,
"cds_start": -4,
"cds_end": null,
"cds_length": 1515,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4631,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "SLC1A1",
"gene_hgnc_id": 10939,
"hgvs_c": "c.767+1634A>C",
"hgvs_p": null,
"transcript": "XM_017015043.2",
"protein_id": "XP_016870532.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 488,
"cds_start": -4,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3590,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "SLC1A1",
"gene_hgnc_id": 10939,
"hgvs_c": "c.734+8A>C",
"hgvs_p": null,
"transcript": "XM_011518010.2",
"protein_id": "XP_011516312.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 477,
"cds_start": -4,
"cds_end": null,
"cds_length": 1434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3557,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC1A1",
"gene_hgnc_id": 10939,
"dbsnp": "rs12682807",
"frequency_reference_population": 0.10720221,
"hom_count_reference_population": 10104,
"allele_count_reference_population": 167857,
"gnomad_exomes_af": 0.109469,
"gnomad_genomes_af": 0.0861625,
"gnomad_exomes_ac": 154736,
"gnomad_genomes_ac": 13121,
"gnomad_exomes_homalt": 9271,
"gnomad_genomes_homalt": 833,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7799999713897705,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.78,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.832,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000223730670469557,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000262352.8",
"gene_symbol": "SLC1A1",
"hgnc_id": 10939,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.875+8A>C",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000485616.5",
"gene_symbol": "SPATA6L",
"hgnc_id": 25472,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.*782-19634T>G",
"hgvs_p": null
}
],
"clinvar_disease": "Dicarboxylic aminoaciduria,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "Dicarboxylic aminoaciduria|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}