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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: 3-57277901-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=57277901&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 57277901,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000487349.6",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASB14",
"gene_hgnc_id": 19766,
"hgvs_c": "c.1451T>C",
"hgvs_p": "p.Leu484Ser",
"transcript": "NM_001142733.3",
"protein_id": "NP_001136205.2",
"transcript_support_level": null,
"aa_start": 484,
"aa_end": null,
"aa_length": 587,
"cds_start": 1451,
"cds_end": null,
"cds_length": 1764,
"cdna_start": 1575,
"cdna_end": null,
"cdna_length": 3187,
"mane_select": "ENST00000487349.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASB14",
"gene_hgnc_id": 19766,
"hgvs_c": "c.1451T>C",
"hgvs_p": "p.Leu484Ser",
"transcript": "ENST00000487349.6",
"protein_id": "ENSP00000419199.1",
"transcript_support_level": 1,
"aa_start": 484,
"aa_end": null,
"aa_length": 587,
"cds_start": 1451,
"cds_end": null,
"cds_length": 1764,
"cdna_start": 1575,
"cdna_end": null,
"cdna_length": 3187,
"mane_select": "NM_001142733.3",
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASB14",
"gene_hgnc_id": 19766,
"hgvs_c": "n.596T>C",
"hgvs_p": null,
"transcript": "ENST00000515033.1",
"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": 909,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASB14",
"gene_hgnc_id": 19766,
"hgvs_c": "c.596T>C",
"hgvs_p": "p.Leu199Ser",
"transcript": "NM_130387.5",
"protein_id": "NP_569058.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 302,
"cds_start": 596,
"cds_end": null,
"cds_length": 909,
"cdna_start": 596,
"cdna_end": null,
"cdna_length": 2199,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASB14",
"gene_hgnc_id": 19766,
"hgvs_c": "c.1451T>C",
"hgvs_p": "p.Leu484Ser",
"transcript": "XM_017005736.3",
"protein_id": "XP_016861225.1",
"transcript_support_level": null,
"aa_start": 484,
"aa_end": null,
"aa_length": 587,
"cds_start": 1451,
"cds_end": null,
"cds_length": 1764,
"cdna_start": 1578,
"cdna_end": null,
"cdna_length": 1913,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ASB14",
"gene_hgnc_id": 19766,
"hgvs_c": "c.1451T>C",
"hgvs_p": "p.Leu484Ser",
"transcript": "XM_017005737.3",
"protein_id": "XP_016861226.1",
"transcript_support_level": null,
"aa_start": 484,
"aa_end": null,
"aa_length": 587,
"cds_start": 1451,
"cds_end": null,
"cds_length": 1764,
"cdna_start": 1524,
"cdna_end": null,
"cdna_length": 1859,
"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": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "n.*329A>G",
"hgvs_p": null,
"transcript": "ENST00000650354.1",
"protein_id": "ENSP00000498115.1",
"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": 2821,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC105377102",
"gene_hgnc_id": null,
"hgvs_c": "n.451A>G",
"hgvs_p": null,
"transcript": "NR_135535.1",
"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": 677,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APPL1",
"gene_hgnc_id": 24035,
"hgvs_c": "n.*329A>G",
"hgvs_p": null,
"transcript": "ENST00000650354.1",
"protein_id": "ENSP00000498115.1",
"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": 2821,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ASB14",
"gene_hgnc_id": 19766,
"dbsnp": "rs778511259",
"frequency_reference_population": 0.000008062825,
"hom_count_reference_population": 0,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.00000136975,
"gnomad_genomes_af": 0.0000722657,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3637945055961609,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.256,
"revel_prediction": "Benign",
"alphamissense_score": 0.5481,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.24,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.008,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "ENST00000487349.6",
"gene_symbol": "ASB14",
"hgnc_id": 19766,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1451T>C",
"hgvs_p": "p.Leu484Ser"
},
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "NR_135535.1",
"gene_symbol": "LOC105377102",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.451A>G",
"hgvs_p": null
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000650354.1",
"gene_symbol": "APPL1",
"hgnc_id": 24035,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "n.*329A>G",
"hgvs_p": null
}
],
"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
}