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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: 2-86507546-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=86507546&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 86507546,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001198954.1",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHMP3",
"gene_hgnc_id": 29865,
"hgvs_c": "c.456C>A",
"hgvs_p": "p.Asp152Glu",
"transcript": "NM_016079.4",
"protein_id": "NP_057163.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 222,
"cds_start": 456,
"cds_end": null,
"cds_length": 669,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000263856.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016079.4"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHMP3",
"gene_hgnc_id": 29865,
"hgvs_c": "c.456C>A",
"hgvs_p": "p.Asp152Glu",
"transcript": "ENST00000263856.9",
"protein_id": "ENSP00000263856.4",
"transcript_support_level": 1,
"aa_start": 152,
"aa_end": null,
"aa_length": 222,
"cds_start": 456,
"cds_end": null,
"cds_length": 669,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016079.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000263856.9"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103-CHMP3",
"gene_hgnc_id": 38847,
"hgvs_c": "c.543C>A",
"hgvs_p": "p.Asp181Glu",
"transcript": "ENST00000604011.5",
"protein_id": "ENSP00000474823.1",
"transcript_support_level": 2,
"aa_start": 181,
"aa_end": null,
"aa_length": 251,
"cds_start": 543,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000604011.5"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103-CHMP3",
"gene_hgnc_id": 38847,
"hgvs_c": "c.543C>A",
"hgvs_p": "p.Asp181Glu",
"transcript": "NM_001198954.1",
"protein_id": "NP_001185883.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 251,
"cds_start": 543,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001198954.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHMP3",
"gene_hgnc_id": 29865,
"hgvs_c": "c.471C>A",
"hgvs_p": "p.Asp157Glu",
"transcript": "ENST00000953402.1",
"protein_id": "ENSP00000623461.1",
"transcript_support_level": null,
"aa_start": 157,
"aa_end": null,
"aa_length": 227,
"cds_start": 471,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953402.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHMP3",
"gene_hgnc_id": 29865,
"hgvs_c": "c.456C>A",
"hgvs_p": "p.Asp152Glu",
"transcript": "ENST00000953404.1",
"protein_id": "ENSP00000623463.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 207,
"cds_start": 456,
"cds_end": null,
"cds_length": 624,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953404.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHMP3",
"gene_hgnc_id": 29865,
"hgvs_c": "c.336C>A",
"hgvs_p": "p.Asp112Glu",
"transcript": "NM_001193517.2",
"protein_id": "NP_001180446.1",
"transcript_support_level": null,
"aa_start": 112,
"aa_end": null,
"aa_length": 182,
"cds_start": 336,
"cds_end": null,
"cds_length": 549,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001193517.2"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHMP3",
"gene_hgnc_id": 29865,
"hgvs_c": "c.336C>A",
"hgvs_p": "p.Asp112Glu",
"transcript": "ENST00000409727.5",
"protein_id": "ENSP00000387045.1",
"transcript_support_level": 2,
"aa_start": 112,
"aa_end": null,
"aa_length": 182,
"cds_start": 336,
"cds_end": null,
"cds_length": 549,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409727.5"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHMP3",
"gene_hgnc_id": 29865,
"hgvs_c": "c.258C>A",
"hgvs_p": "p.Asp86Glu",
"transcript": "NM_001005753.3",
"protein_id": "NP_001005753.1",
"transcript_support_level": null,
"aa_start": 86,
"aa_end": null,
"aa_length": 156,
"cds_start": 258,
"cds_end": null,
"cds_length": 471,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001005753.3"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHMP3",
"gene_hgnc_id": 29865,
"hgvs_c": "c.258C>A",
"hgvs_p": "p.Asp86Glu",
"transcript": "ENST00000409225.2",
"protein_id": "ENSP00000386590.2",
"transcript_support_level": 2,
"aa_start": 86,
"aa_end": null,
"aa_length": 156,
"cds_start": 258,
"cds_end": null,
"cds_length": 471,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409225.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "CHMP3",
"gene_hgnc_id": 29865,
"hgvs_c": "c.287-1597C>A",
"hgvs_p": null,
"transcript": "ENST00000953403.1",
"protein_id": "ENSP00000623462.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 143,
"cds_start": null,
"cds_end": null,
"cds_length": 432,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953403.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHMP3",
"gene_hgnc_id": 29865,
"hgvs_c": "n.485C>A",
"hgvs_p": null,
"transcript": "ENST00000393773.7",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000393773.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHMP3",
"gene_hgnc_id": 29865,
"hgvs_c": "n.471C>A",
"hgvs_p": null,
"transcript": "ENST00000409810.6",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000409810.6"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHMP3",
"gene_hgnc_id": 29865,
"hgvs_c": "n.2226C>A",
"hgvs_p": null,
"transcript": "ENST00000494623.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000494623.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHMP3",
"gene_hgnc_id": 29865,
"hgvs_c": "n.310C>A",
"hgvs_p": null,
"transcript": "NR_036454.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_036454.2"
}
],
"gene_symbol": "RNF103-CHMP3",
"gene_hgnc_id": 38847,
"dbsnp": "rs199633699",
"frequency_reference_population": 0.00018710487,
"hom_count_reference_population": 0,
"allele_count_reference_population": 302,
"gnomad_exomes_af": 0.000199063,
"gnomad_genomes_af": 0.0000722648,
"gnomad_exomes_ac": 291,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.016735613346099854,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.322,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0954,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.901,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001198954.1",
"gene_symbol": "RNF103-CHMP3",
"hgnc_id": 38847,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.543C>A",
"hgvs_p": "p.Asp181Glu"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_016079.4",
"gene_symbol": "CHMP3",
"hgnc_id": 29865,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.456C>A",
"hgvs_p": "p.Asp152Glu"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}