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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: 7-105614172-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=105614172&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ATXN7L1",
"hgnc_id": 22210,
"hgvs_c": "c.2162C>T",
"hgvs_p": "p.Ser721Leu",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_001385596.1",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000295921",
"hgnc_id": null,
"hgvs_c": "n.109-23560G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000733939.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 122,
"alphamissense_prediction": null,
"alphamissense_score": 0.0687,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.51,
"chr": "7",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.058823227882385254,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 861,
"aa_ref": "S",
"aa_start": 721,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5707,
"cdna_start": 2203,
"cds_end": null,
"cds_length": 2586,
"cds_start": 2162,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_020725.2",
"gene_hgnc_id": 22210,
"gene_symbol": "ATXN7L1",
"hgvs_c": "c.2162C>T",
"hgvs_p": "p.Ser721Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000419735.8",
"protein_coding": true,
"protein_id": "NP_065776.1",
"strand": false,
"transcript": "NM_020725.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 861,
"aa_ref": "S",
"aa_start": 721,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5707,
"cdna_start": 2203,
"cds_end": null,
"cds_length": 2586,
"cds_start": 2162,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000419735.8",
"gene_hgnc_id": 22210,
"gene_symbol": "ATXN7L1",
"hgvs_c": "c.2162C>T",
"hgvs_p": "p.Ser721Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_020725.2",
"protein_coding": true,
"protein_id": "ENSP00000410759.3",
"strand": false,
"transcript": "ENST00000419735.8",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 574,
"aa_ref": "S",
"aa_start": 422,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1963,
"cdna_start": 1265,
"cds_end": null,
"cds_length": 1725,
"cds_start": 1265,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000484475.5",
"gene_hgnc_id": 22210,
"gene_symbol": "ATXN7L1",
"hgvs_c": "c.1265C>T",
"hgvs_p": "p.Ser422Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418900.1",
"strand": false,
"transcript": "ENST00000484475.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2732,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000474433.5",
"gene_hgnc_id": 22210,
"gene_symbol": "ATXN7L1",
"hgvs_c": "n.*1737C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000420483.1",
"strand": false,
"transcript": "ENST00000474433.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2732,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000474433.5",
"gene_hgnc_id": 22210,
"gene_symbol": "ATXN7L1",
"hgvs_c": "n.*1737C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000420483.1",
"strand": false,
"transcript": "ENST00000474433.5",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 862,
"aa_ref": "S",
"aa_start": 721,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5710,
"cdna_start": 2203,
"cds_end": null,
"cds_length": 2589,
"cds_start": 2162,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001385596.1",
"gene_hgnc_id": 22210,
"gene_symbol": "ATXN7L1",
"hgvs_c": "c.2162C>T",
"hgvs_p": "p.Ser721Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001372525.1",
"strand": false,
"transcript": "NM_001385596.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 742,
"aa_ref": "S",
"aa_start": 597,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2324,
"cdna_start": 1885,
"cds_end": null,
"cds_length": 2229,
"cds_start": 1790,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000472195.1",
"gene_hgnc_id": 22210,
"gene_symbol": "ATXN7L1",
"hgvs_c": "c.1790C>T",
"hgvs_p": "p.Ser597Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000419566.1",
"strand": false,
"transcript": "ENST00000472195.1",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 738,
"aa_ref": "S",
"aa_start": 597,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5418,
"cdna_start": 1911,
"cds_end": null,
"cds_length": 2217,
"cds_start": 1790,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_138495.2",
"gene_hgnc_id": 22210,
"gene_symbol": "ATXN7L1",
"hgvs_c": "c.1790C>T",
"hgvs_p": "p.Ser597Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_612504.1",
"strand": false,
"transcript": "NM_138495.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 738,
"aa_ref": "S",
"aa_start": 597,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2426,
"cdna_start": 1918,
"cds_end": null,
"cds_length": 2217,
"cds_start": 1790,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000477775.5",
"gene_hgnc_id": 22210,
"gene_symbol": "ATXN7L1",
"hgvs_c": "c.1790C>T",
"hgvs_p": "p.Ser597Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418476.1",
"strand": false,
"transcript": "ENST00000477775.5",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 657,
"aa_ref": "S",
"aa_start": 505,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2882,
"cdna_start": 2184,
"cds_end": null,
"cds_length": 1974,
"cds_start": 1514,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001318229.2",
"gene_hgnc_id": 22210,
"gene_symbol": "ATXN7L1",
"hgvs_c": "c.1514C>T",
"hgvs_p": "p.Ser505Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001305158.1",
"strand": false,
"transcript": "NM_001318229.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 548,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000733939.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000295921",
"hgvs_c": "n.109-23560G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000733939.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 408,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000733940.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000295921",
"hgvs_c": "n.257+16712G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000733940.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs562318903",
"effect": "missense_variant",
"frequency_reference_population": 0.00007862304,
"gene_hgnc_id": 22210,
"gene_symbol": "ATXN7L1",
"gnomad_exomes_ac": 111,
"gnomad_exomes_af": 0.0000793206,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 11,
"gnomad_genomes_af": 0.0000722145,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.132,
"pos": 105614172,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.043,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001385596.1"
}
]
}