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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: 2-48451059-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=48451059&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 48451059,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001135629.3",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPP1R21",
"gene_hgnc_id": 30595,
"hgvs_c": "c.109A>T",
"hgvs_p": "p.Asn37Tyr",
"transcript": "NM_001135629.3",
"protein_id": "NP_001129101.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 780,
"cds_start": 109,
"cds_end": null,
"cds_length": 2343,
"cdna_start": 297,
"cdna_end": null,
"cdna_length": 3173,
"mane_select": "ENST00000294952.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPP1R21",
"gene_hgnc_id": 30595,
"hgvs_c": "c.109A>T",
"hgvs_p": "p.Asn37Tyr",
"transcript": "ENST00000294952.13",
"protein_id": "ENSP00000294952.8",
"transcript_support_level": 1,
"aa_start": 37,
"aa_end": null,
"aa_length": 780,
"cds_start": 109,
"cds_end": null,
"cds_length": 2343,
"cdna_start": 297,
"cdna_end": null,
"cdna_length": 3173,
"mane_select": "NM_001135629.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPP1R21",
"gene_hgnc_id": 30595,
"hgvs_c": "c.109A>T",
"hgvs_p": "p.Asn37Tyr",
"transcript": "ENST00000281394.8",
"protein_id": "ENSP00000281394.4",
"transcript_support_level": 1,
"aa_start": 37,
"aa_end": null,
"aa_length": 769,
"cds_start": 109,
"cds_end": null,
"cds_length": 2310,
"cdna_start": 294,
"cdna_end": null,
"cdna_length": 3137,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPP1R21",
"gene_hgnc_id": 30595,
"hgvs_c": "c.109A>T",
"hgvs_p": "p.Asn37Tyr",
"transcript": "ENST00000449090.6",
"protein_id": "ENSP00000415696.2",
"transcript_support_level": 1,
"aa_start": 37,
"aa_end": null,
"aa_length": 738,
"cds_start": 109,
"cds_end": null,
"cds_length": 2217,
"cdna_start": 294,
"cdna_end": null,
"cdna_length": 3049,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPP1R21",
"gene_hgnc_id": 30595,
"hgvs_c": "c.109A>T",
"hgvs_p": "p.Asn37Tyr",
"transcript": "NM_152994.5",
"protein_id": "NP_694539.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 769,
"cds_start": 109,
"cds_end": null,
"cds_length": 2310,
"cdna_start": 297,
"cdna_end": null,
"cdna_length": 3140,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPP1R21",
"gene_hgnc_id": 30595,
"hgvs_c": "c.109A>T",
"hgvs_p": "p.Asn37Tyr",
"transcript": "NM_001193475.2",
"protein_id": "NP_001180404.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 738,
"cds_start": 109,
"cds_end": null,
"cds_length": 2217,
"cdna_start": 297,
"cdna_end": null,
"cdna_length": 3047,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPP1R21",
"gene_hgnc_id": 30595,
"hgvs_c": "c.109A>T",
"hgvs_p": "p.Asn37Tyr",
"transcript": "XM_047443254.1",
"protein_id": "XP_047299210.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 459,
"cds_start": 109,
"cds_end": null,
"cds_length": 1380,
"cdna_start": 297,
"cdna_end": null,
"cdna_length": 1595,
"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": 2,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPP1R21",
"gene_hgnc_id": 30595,
"hgvs_c": "n.109A>T",
"hgvs_p": null,
"transcript": "ENST00000416913.5",
"protein_id": "ENSP00000414130.1",
"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": 3208,
"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": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPP1R21",
"gene_hgnc_id": 30595,
"hgvs_c": "n.-30A>T",
"hgvs_p": null,
"transcript": "ENST00000431614.5",
"protein_id": "ENSP00000406283.1",
"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": 2481,
"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": 2,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPP1R21",
"gene_hgnc_id": 30595,
"hgvs_c": "n.297A>T",
"hgvs_p": null,
"transcript": "NR_024188.3",
"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": 3212,
"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": 2,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPP1R21",
"gene_hgnc_id": 30595,
"hgvs_c": "n.297A>T",
"hgvs_p": null,
"transcript": "XR_007069367.1",
"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": 2383,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPP1R21",
"gene_hgnc_id": 30595,
"hgvs_c": "c.-30A>T",
"hgvs_p": null,
"transcript": "ENST00000421486.1",
"protein_id": "ENSP00000410955.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 39,
"cds_start": -4,
"cds_end": null,
"cds_length": 122,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 545,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPP1R21",
"gene_hgnc_id": 30595,
"hgvs_c": "n.-30A>T",
"hgvs_p": null,
"transcript": "ENST00000431614.5",
"protein_id": "ENSP00000406283.1",
"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": 2481,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PPP1R21",
"gene_hgnc_id": 30595,
"dbsnp": null,
"frequency_reference_population": 6.8429125e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84291e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.34242695569992065,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.23,
"revel_prediction": "Benign",
"alphamissense_score": 0.2039,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.17,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.09,
"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": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001135629.3",
"gene_symbol": "PPP1R21",
"hgnc_id": 30595,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.109A>T",
"hgvs_p": "p.Asn37Tyr"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}