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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: 1-2629420-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=2629420&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "MMEL1",
"hgnc_id": 14668,
"hgvs_c": "c.65C>T",
"hgvs_p": "p.Pro22Leu",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_033467.4",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "MMEL1-AS1",
"hgnc_id": 40695,
"hgvs_c": "n.183+517G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -4,
"transcript": "ENST00000427302.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_score": -4,
"allele_count_reference_population": 30,
"alphamissense_prediction": null,
"alphamissense_score": 0.0823,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.39,
"chr": "1",
"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": 0.051489949226379395,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 779,
"aa_ref": "P",
"aa_start": 22,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2879,
"cdna_start": 253,
"cds_end": null,
"cds_length": 2340,
"cds_start": 65,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_033467.4",
"gene_hgnc_id": 14668,
"gene_symbol": "MMEL1",
"hgvs_c": "c.65C>T",
"hgvs_p": "p.Pro22Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000378412.8",
"protein_coding": true,
"protein_id": "NP_258428.2",
"strand": false,
"transcript": "NM_033467.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 779,
"aa_ref": "P",
"aa_start": 22,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2879,
"cdna_start": 253,
"cds_end": null,
"cds_length": 2340,
"cds_start": 65,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000378412.8",
"gene_hgnc_id": 14668,
"gene_symbol": "MMEL1",
"hgvs_c": "c.65C>T",
"hgvs_p": "p.Pro22Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_033467.4",
"protein_coding": true,
"protein_id": "ENSP00000367668.3",
"strand": false,
"transcript": "ENST00000378412.8",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 622,
"aa_ref": "P",
"aa_start": 22,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1943,
"cdna_start": 75,
"cds_end": null,
"cds_length": 1869,
"cds_start": 65,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000502556.5",
"gene_hgnc_id": 14668,
"gene_symbol": "MMEL1",
"hgvs_c": "c.65C>T",
"hgvs_p": "p.Pro22Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000422492.1",
"strand": false,
"transcript": "ENST00000502556.5",
"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": 2443,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 23,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000504800.5",
"gene_hgnc_id": 14668,
"gene_symbol": "MMEL1",
"hgvs_c": "n.65C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000425477.1",
"strand": false,
"transcript": "ENST00000504800.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 625,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000427302.2",
"gene_hgnc_id": 40695,
"gene_symbol": "MMEL1-AS1",
"hgvs_c": "n.183+517G>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": "ENST00000427302.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 789,
"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": "ENST00000723522.1",
"gene_hgnc_id": 40695,
"gene_symbol": "MMEL1-AS1",
"hgvs_c": "n.216+517G>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": "ENST00000723522.1",
"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": 478,
"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": "ENST00000723523.1",
"gene_hgnc_id": 40695,
"gene_symbol": "MMEL1-AS1",
"hgvs_c": "n.213+517G>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": "ENST00000723523.1",
"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": 470,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000723524.1",
"gene_hgnc_id": 40695,
"gene_symbol": "MMEL1-AS1",
"hgvs_c": "n.60+517G>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": "ENST00000723524.1",
"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": 519,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000723525.1",
"gene_hgnc_id": 40695,
"gene_symbol": "MMEL1-AS1",
"hgvs_c": "n.80+281G>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": "ENST00000723525.1",
"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": 587,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_183343.1",
"gene_hgnc_id": 40695,
"gene_symbol": "MMEL1-AS1",
"hgvs_c": "n.148+517G>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": "NR_183343.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs760779285",
"effect": "missense_variant",
"frequency_reference_population": 0.000019412199,
"gene_hgnc_id": 14668,
"gene_symbol": "MMEL1",
"gnomad_exomes_ac": 27,
"gnomad_exomes_af": 0.0000193788,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197179,
"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": -0.689,
"pos": 2629420,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.151,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_033467.4"
}
]
}