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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: 16-23544679-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=23544679&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 23544679,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000449606.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "c.320G>A",
"hgvs_p": "p.Arg107His",
"transcript": "NM_001083614.2",
"protein_id": "NP_001077083.1",
"transcript_support_level": null,
"aa_start": 107,
"aa_end": null,
"aa_length": 523,
"cds_start": 320,
"cds_end": null,
"cds_length": 1572,
"cdna_start": 327,
"cdna_end": null,
"cdna_length": 5196,
"mane_select": "ENST00000449606.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "c.320G>A",
"hgvs_p": "p.Arg107His",
"transcript": "ENST00000449606.7",
"protein_id": "ENSP00000395196.2",
"transcript_support_level": 1,
"aa_start": 107,
"aa_end": null,
"aa_length": 523,
"cds_start": 320,
"cds_end": null,
"cds_length": 1572,
"cdna_start": 327,
"cdna_end": null,
"cdna_length": 5196,
"mane_select": "NM_001083614.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "c.320G>A",
"hgvs_p": "p.Arg107His",
"transcript": "ENST00000563232.1",
"protein_id": "ENSP00000456218.1",
"transcript_support_level": 1,
"aa_start": 107,
"aa_end": null,
"aa_length": 534,
"cds_start": 320,
"cds_end": null,
"cds_length": 1605,
"cdna_start": 321,
"cdna_end": null,
"cdna_length": 1709,
"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": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "n.60-116G>A",
"hgvs_p": null,
"transcript": "ENST00000564987.1",
"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": 2870,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "c.320G>A",
"hgvs_p": "p.Arg107His",
"transcript": "NM_001308211.1",
"protein_id": "NP_001295140.1",
"transcript_support_level": null,
"aa_start": 107,
"aa_end": null,
"aa_length": 534,
"cds_start": 320,
"cds_end": null,
"cds_length": 1605,
"cdna_start": 352,
"cdna_end": null,
"cdna_length": 1744,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "c.320G>A",
"hgvs_p": "p.Arg107His",
"transcript": "ENST00000564501.5",
"protein_id": "ENSP00000457107.1",
"transcript_support_level": 5,
"aa_start": 107,
"aa_end": null,
"aa_length": 506,
"cds_start": 320,
"cds_end": null,
"cds_length": 1521,
"cdna_start": 708,
"cdna_end": null,
"cdna_length": 2027,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "c.248G>A",
"hgvs_p": "p.Arg83His",
"transcript": "XM_011545738.2",
"protein_id": "XP_011544040.1",
"transcript_support_level": null,
"aa_start": 83,
"aa_end": null,
"aa_length": 499,
"cds_start": 248,
"cds_end": null,
"cds_length": 1500,
"cdna_start": 642,
"cdna_end": null,
"cdna_length": 5511,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "n.380G>A",
"hgvs_p": null,
"transcript": "ENST00000561859.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 518,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "n.*193G>A",
"hgvs_p": null,
"transcript": "ENST00000562581.5",
"protein_id": "ENSP00000455519.1",
"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": 533,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "n.504G>A",
"hgvs_p": null,
"transcript": "ENST00000564461.5",
"protein_id": null,
"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": 675,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "n.*100G>A",
"hgvs_p": null,
"transcript": "ENST00000564668.5",
"protein_id": "ENSP00000455789.1",
"transcript_support_level": 4,
"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": 627,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "n.*197G>A",
"hgvs_p": null,
"transcript": "ENST00000564997.1",
"protein_id": "ENSP00000455875.1",
"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": 572,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "n.287G>A",
"hgvs_p": null,
"transcript": "ENST00000566017.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 539,
"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": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "n.320G>A",
"hgvs_p": null,
"transcript": "ENST00000674054.1",
"protein_id": "ENSP00000501251.1",
"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": 3840,
"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": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "n.327G>A",
"hgvs_p": null,
"transcript": "NR_003501.2",
"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": 3841,
"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": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "n.642G>A",
"hgvs_p": null,
"transcript": "XR_001751841.1",
"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": 4156,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "n.*193G>A",
"hgvs_p": null,
"transcript": "ENST00000562581.5",
"protein_id": "ENSP00000455519.1",
"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": 533,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "n.*100G>A",
"hgvs_p": null,
"transcript": "ENST00000564668.5",
"protein_id": "ENSP00000455789.1",
"transcript_support_level": 4,
"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": 627,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"hgvs_c": "n.*197G>A",
"hgvs_p": null,
"transcript": "ENST00000564997.1",
"protein_id": "ENSP00000455875.1",
"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": 572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EARS2",
"gene_hgnc_id": 29419,
"dbsnp": "rs1021330566",
"frequency_reference_population": 0.000016814321,
"hom_count_reference_population": 0,
"allele_count_reference_population": 27,
"gnomad_exomes_af": 0.0000178876,
"gnomad_genomes_af": 0.00000656814,
"gnomad_exomes_ac": 26,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2180166244506836,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.017,
"revel_prediction": "Benign",
"alphamissense_score": 0.1193,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.464,
"phylop100way_prediction": "Benign",
"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": 13,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP5_Very_Strong,BP4",
"acmg_by_gene": [
{
"score": 13,
"benign_score": 1,
"pathogenic_score": 14,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP5_Very_Strong",
"BP4"
],
"verdict": "Pathogenic",
"transcript": "ENST00000449606.7",
"gene_symbol": "EARS2",
"hgnc_id": 29419,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.320G>A",
"hgvs_p": "p.Arg107His"
}
],
"clinvar_disease": "Leukoencephalopathy-thalamus and brainstem anomalies-high lactate syndrome,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3 LP:3",
"phenotype_combined": "not provided|Leukoencephalopathy-thalamus and brainstem anomalies-high lactate syndrome",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}