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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: 4-70705219-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=70705219&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 70705219,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001130709.2",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY3",
"gene_hgnc_id": 30285,
"hgvs_c": "c.283C>T",
"hgvs_p": "p.Pro95Ser",
"transcript": "ENST00000417478.6",
"protein_id": "ENSP00000399771.2",
"transcript_support_level": 1,
"aa_start": 95,
"aa_end": null,
"aa_length": 506,
"cds_start": 283,
"cds_end": null,
"cds_length": 1521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000417478.6"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY3",
"gene_hgnc_id": 30285,
"hgvs_c": "c.283C>T",
"hgvs_p": "p.Pro95Ser",
"transcript": "NM_001130709.2",
"protein_id": "NP_001124181.1",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 506,
"cds_start": 283,
"cds_end": null,
"cds_length": 1521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001130709.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY3",
"gene_hgnc_id": 30285,
"hgvs_c": "c.283C>T",
"hgvs_p": "p.Pro95Ser",
"transcript": "ENST00000514898.1",
"protein_id": "ENSP00000426165.1",
"transcript_support_level": 4,
"aa_start": 95,
"aa_end": null,
"aa_length": 97,
"cds_start": 283,
"cds_end": null,
"cds_length": 294,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000514898.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY3",
"gene_hgnc_id": 30285,
"hgvs_c": "c.283C>T",
"hgvs_p": "p.Pro95Ser",
"transcript": "XM_011531750.3",
"protein_id": "XP_011530052.1",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 680,
"cds_start": 283,
"cds_end": null,
"cds_length": 2043,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531750.3"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY3",
"gene_hgnc_id": 30285,
"hgvs_c": "c.283C>T",
"hgvs_p": "p.Pro95Ser",
"transcript": "XM_047449825.1",
"protein_id": "XP_047305781.1",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 680,
"cds_start": 283,
"cds_end": null,
"cds_length": 2043,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047449825.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY3",
"gene_hgnc_id": 30285,
"hgvs_c": "c.283C>T",
"hgvs_p": "p.Pro95Ser",
"transcript": "XM_011531751.4",
"protein_id": "XP_011530053.1",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 657,
"cds_start": 283,
"cds_end": null,
"cds_length": 1974,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531751.4"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY3",
"gene_hgnc_id": 30285,
"hgvs_c": "c.283C>T",
"hgvs_p": "p.Pro95Ser",
"transcript": "XM_047449827.1",
"protein_id": "XP_047305783.1",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 586,
"cds_start": 283,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047449827.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY3",
"gene_hgnc_id": 30285,
"hgvs_c": "c.283C>T",
"hgvs_p": "p.Pro95Ser",
"transcript": "XM_047449828.1",
"protein_id": "XP_047305784.1",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 557,
"cds_start": 283,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047449828.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY3",
"gene_hgnc_id": 30285,
"hgvs_c": "c.283C>T",
"hgvs_p": "p.Pro95Ser",
"transcript": "XM_011531755.4",
"protein_id": "XP_011530057.1",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 529,
"cds_start": 283,
"cds_end": null,
"cds_length": 1590,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531755.4"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY3",
"gene_hgnc_id": 30285,
"hgvs_c": "c.283C>T",
"hgvs_p": "p.Pro95Ser",
"transcript": "XM_011531756.4",
"protein_id": "XP_011530058.1",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 518,
"cds_start": 283,
"cds_end": null,
"cds_length": 1557,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531756.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY3",
"gene_hgnc_id": 30285,
"hgvs_c": "c.-86C>T",
"hgvs_p": null,
"transcript": "ENST00000947599.1",
"protein_id": "ENSP00000617658.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 620,
"cds_start": null,
"cds_end": null,
"cds_length": 1863,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947599.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY3",
"gene_hgnc_id": 30285,
"hgvs_c": "c.-5092C>T",
"hgvs_p": null,
"transcript": "XM_005265656.4",
"protein_id": "XP_005265713.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 638,
"cds_start": null,
"cds_end": null,
"cds_length": 1917,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005265656.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "RUFY3",
"gene_hgnc_id": 30285,
"hgvs_c": "c.-15+744C>T",
"hgvs_p": null,
"transcript": "ENST00000503876.5",
"protein_id": "ENSP00000426734.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 154,
"cds_start": null,
"cds_end": null,
"cds_length": 465,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000503876.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY3",
"gene_hgnc_id": 30285,
"hgvs_c": "n.481C>T",
"hgvs_p": null,
"transcript": "XR_007096384.1",
"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": "XR_007096384.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY3",
"gene_hgnc_id": 30285,
"hgvs_c": "n.481C>T",
"hgvs_p": null,
"transcript": "XR_007096385.1",
"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": "XR_007096385.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY3",
"gene_hgnc_id": 30285,
"hgvs_c": "n.481C>T",
"hgvs_p": null,
"transcript": "XR_938709.4",
"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": "XR_938709.4"
}
],
"gene_symbol": "RUFY3",
"gene_hgnc_id": 30285,
"dbsnp": "rs1333124003",
"frequency_reference_population": 0.000008209742,
"hom_count_reference_population": 0,
"allele_count_reference_population": 12,
"gnomad_exomes_af": 0.00000839742,
"gnomad_genomes_af": 0.0000065897,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2679821252822876,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": 0.105,
"revel_prediction": "Benign",
"alphamissense_score": 0.2566,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.223,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001130709.2",
"gene_symbol": "RUFY3",
"hgnc_id": 30285,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.283C>T",
"hgvs_p": "p.Pro95Ser"
}
],
"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
}