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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: 2-86529388-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=86529388&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "RNF103-CHMP3",
"hgnc_id": 38847,
"hgvs_c": "c.203G>A",
"hgvs_p": "p.Arg68Lys",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_001198954.1",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CHMP3",
"hgnc_id": 29865,
"hgvs_c": "c.116G>A",
"hgvs_p": "p.Arg39Lys",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_016079.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.3287,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.01,
"chr": "2",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5795882344245911,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 222,
"aa_ref": "R",
"aa_start": 39,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3138,
"cdna_start": 211,
"cds_end": null,
"cds_length": 669,
"cds_start": 116,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_016079.4",
"gene_hgnc_id": 29865,
"gene_symbol": "CHMP3",
"hgvs_c": "c.116G>A",
"hgvs_p": "p.Arg39Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000263856.9",
"protein_coding": true,
"protein_id": "NP_057163.1",
"strand": false,
"transcript": "NM_016079.4",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 222,
"aa_ref": "R",
"aa_start": 39,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3138,
"cdna_start": 211,
"cds_end": null,
"cds_length": 669,
"cds_start": 116,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000263856.9",
"gene_hgnc_id": 29865,
"gene_symbol": "CHMP3",
"hgvs_c": "c.116G>A",
"hgvs_p": "p.Arg39Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_016079.4",
"protein_coding": true,
"protein_id": "ENSP00000263856.4",
"strand": false,
"transcript": "ENST00000263856.9",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 251,
"aa_ref": "R",
"aa_start": 68,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1135,
"cdna_start": 446,
"cds_end": null,
"cds_length": 756,
"cds_start": 203,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000604011.5",
"gene_hgnc_id": 38847,
"gene_symbol": "RNF103-CHMP3",
"hgvs_c": "c.203G>A",
"hgvs_p": "p.Arg68Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000474823.1",
"strand": false,
"transcript": "ENST00000604011.5",
"transcript_support_level": 2
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 251,
"aa_ref": "R",
"aa_start": 68,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3373,
"cdna_start": 446,
"cds_end": null,
"cds_length": 756,
"cds_start": 203,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001198954.1",
"gene_hgnc_id": 38847,
"gene_symbol": "RNF103-CHMP3",
"hgvs_c": "c.203G>A",
"hgvs_p": "p.Arg68Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001185883.1",
"strand": false,
"transcript": "NM_001198954.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 227,
"aa_ref": "R",
"aa_start": 39,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2146,
"cdna_start": 275,
"cds_end": null,
"cds_length": 684,
"cds_start": 116,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000953402.1",
"gene_hgnc_id": 29865,
"gene_symbol": "CHMP3",
"hgvs_c": "c.116G>A",
"hgvs_p": "p.Arg39Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000623461.1",
"strand": false,
"transcript": "ENST00000953402.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 220,
"aa_ref": "R",
"aa_start": 146,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 805,
"cdna_start": 579,
"cds_end": null,
"cds_length": 663,
"cds_start": 437,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000440757.2",
"gene_hgnc_id": 38847,
"gene_symbol": "RNF103-CHMP3",
"hgvs_c": "c.437G>A",
"hgvs_p": "p.Arg146Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000392995.2",
"strand": false,
"transcript": "ENST00000440757.2",
"transcript_support_level": 3
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 207,
"aa_ref": "R",
"aa_start": 39,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 906,
"cdna_start": 200,
"cds_end": null,
"cds_length": 624,
"cds_start": 116,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000953404.1",
"gene_hgnc_id": 29865,
"gene_symbol": "CHMP3",
"hgvs_c": "c.116G>A",
"hgvs_p": "p.Arg39Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000623463.1",
"strand": false,
"transcript": "ENST00000953404.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 182,
"aa_ref": "R",
"aa_start": 39,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3018,
"cdna_start": 211,
"cds_end": null,
"cds_length": 549,
"cds_start": 116,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001193517.2",
"gene_hgnc_id": 29865,
"gene_symbol": "CHMP3",
"hgvs_c": "c.116G>A",
"hgvs_p": "p.Arg39Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001180446.1",
"strand": false,
"transcript": "NM_001193517.2",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 182,
"aa_ref": "R",
"aa_start": 39,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1851,
"cdna_start": 142,
"cds_end": null,
"cds_length": 549,
"cds_start": 116,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000409727.5",
"gene_hgnc_id": 29865,
"gene_symbol": "CHMP3",
"hgvs_c": "c.116G>A",
"hgvs_p": "p.Arg39Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000387045.1",
"strand": false,
"transcript": "ENST00000409727.5",
"transcript_support_level": 2
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 143,
"aa_ref": "R",
"aa_start": 39,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1818,
"cdna_start": 226,
"cds_end": null,
"cds_length": 432,
"cds_start": 116,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000953403.1",
"gene_hgnc_id": 29865,
"gene_symbol": "CHMP3",
"hgvs_c": "c.116G>A",
"hgvs_p": "p.Arg39Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000623462.1",
"strand": false,
"transcript": "ENST00000953403.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 156,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3077,
"cdna_start": null,
"cds_end": null,
"cds_length": 471,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001005753.3",
"gene_hgnc_id": 29865,
"gene_symbol": "CHMP3",
"hgvs_c": "c.-83G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001005753.1",
"strand": false,
"transcript": "NM_001005753.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 156,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1099,
"cdna_start": null,
"cds_end": null,
"cds_length": 471,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000409225.2",
"gene_hgnc_id": 29865,
"gene_symbol": "CHMP3",
"hgvs_c": "c.-83G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000386590.2",
"strand": false,
"transcript": "ENST00000409225.2",
"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": 727,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000393773.7",
"gene_hgnc_id": 29865,
"gene_symbol": "CHMP3",
"hgvs_c": "n.145G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000393773.7",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 559,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000409810.6",
"gene_hgnc_id": 29865,
"gene_symbol": "CHMP3",
"hgvs_c": "n.131G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000409810.6",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 436,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000466032.1",
"gene_hgnc_id": 29865,
"gene_symbol": "CHMP3",
"hgvs_c": "n.72G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000466032.1",
"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": 650,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000486404.5",
"gene_hgnc_id": 29865,
"gene_symbol": "CHMP3",
"hgvs_c": "n.378G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000486404.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2897,
"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": "NR_036454.2",
"gene_hgnc_id": 29865,
"gene_symbol": "CHMP3",
"hgvs_c": "n.141-18909G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_036454.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs762716183",
"effect": "missense_variant",
"frequency_reference_population": 6.929709e-7,
"gene_hgnc_id": 38847,
"gene_symbol": "RNF103-CHMP3",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.92971e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.821,
"pos": 86529388,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.384,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001198954.1"
}
]
}