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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: 2-86604086-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=86604086&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 86604086,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_005667.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "c.1815A>C",
"hgvs_p": "p.Glu605Asp",
"transcript": "NM_005667.4",
"protein_id": "NP_005658.1",
"transcript_support_level": null,
"aa_start": 605,
"aa_end": null,
"aa_length": 685,
"cds_start": 1815,
"cds_end": null,
"cds_length": 2058,
"cdna_start": 2794,
"cdna_end": null,
"cdna_length": 3482,
"mane_select": "ENST00000237455.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005667.4"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "c.1815A>C",
"hgvs_p": "p.Glu605Asp",
"transcript": "ENST00000237455.5",
"protein_id": "ENSP00000237455.4",
"transcript_support_level": 1,
"aa_start": 605,
"aa_end": null,
"aa_length": 685,
"cds_start": 1815,
"cds_end": null,
"cds_length": 2058,
"cdna_start": 2794,
"cdna_end": null,
"cdna_length": 3482,
"mane_select": "NM_005667.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000237455.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RNF103-CHMP3",
"gene_hgnc_id": 38847,
"hgvs_c": "c.132+16244A>C",
"hgvs_p": null,
"transcript": "ENST00000604011.5",
"protein_id": "ENSP00000474823.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 251,
"cds_start": null,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1135,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000604011.5"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHMP3-AS1",
"gene_hgnc_id": 55795,
"hgvs_c": "n.80T>G",
"hgvs_p": null,
"transcript": "ENST00000426549.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 1948,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000426549.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "c.1887A>C",
"hgvs_p": "p.Glu629Asp",
"transcript": "ENST00000886122.1",
"protein_id": "ENSP00000556181.1",
"transcript_support_level": null,
"aa_start": 629,
"aa_end": null,
"aa_length": 709,
"cds_start": 1887,
"cds_end": null,
"cds_length": 2130,
"cdna_start": 2878,
"cdna_end": null,
"cdna_length": 3566,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886122.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "c.1830A>C",
"hgvs_p": "p.Glu610Asp",
"transcript": "ENST00000886123.1",
"protein_id": "ENSP00000556182.1",
"transcript_support_level": null,
"aa_start": 610,
"aa_end": null,
"aa_length": 690,
"cds_start": 1830,
"cds_end": null,
"cds_length": 2073,
"cdna_start": 2799,
"cdna_end": null,
"cdna_length": 3490,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886123.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "c.1806A>C",
"hgvs_p": "p.Glu602Asp",
"transcript": "ENST00000949491.1",
"protein_id": "ENSP00000619550.1",
"transcript_support_level": null,
"aa_start": 602,
"aa_end": null,
"aa_length": 682,
"cds_start": 1806,
"cds_end": null,
"cds_length": 2049,
"cdna_start": 2736,
"cdna_end": null,
"cdna_length": 3421,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949491.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "c.1803A>C",
"hgvs_p": "p.Glu601Asp",
"transcript": "NM_001198951.1",
"protein_id": "NP_001185880.1",
"transcript_support_level": null,
"aa_start": 601,
"aa_end": null,
"aa_length": 681,
"cds_start": 1803,
"cds_end": null,
"cds_length": 2046,
"cdna_start": 1818,
"cdna_end": null,
"cdna_length": 2511,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001198951.1"
},
{
"aa_ref": "E",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "c.759A>C",
"hgvs_p": "p.Glu253Asp",
"transcript": "ENST00000949492.1",
"protein_id": "ENSP00000619551.1",
"transcript_support_level": null,
"aa_start": 253,
"aa_end": null,
"aa_length": 333,
"cds_start": 759,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 1086,
"cdna_end": null,
"cdna_length": 1772,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949492.1"
},
{
"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": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RNF103-CHMP3",
"gene_hgnc_id": 38847,
"hgvs_c": "c.132+16244A>C",
"hgvs_p": null,
"transcript": "NM_001198954.1",
"protein_id": "NP_001185883.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 251,
"cds_start": null,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3373,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001198954.1"
},
{
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "RNF103-CHMP3",
"gene_hgnc_id": 38847,
"hgvs_c": "c.366+16244A>C",
"hgvs_p": null,
"transcript": "ENST00000440757.2",
"protein_id": "ENSP00000392995.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 220,
"cds_start": null,
"cds_end": null,
"cds_length": 663,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 805,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000440757.2"
},
{
"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": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "n.3874A>C",
"hgvs_p": null,
"transcript": "ENST00000472030.1",
"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": 4560,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000472030.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHMP3-AS1",
"gene_hgnc_id": 55795,
"hgvs_c": "n.60T>G",
"hgvs_p": null,
"transcript": "ENST00000725270.1",
"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": 537,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000725270.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CHMP3-AS1",
"gene_hgnc_id": 55795,
"hgvs_c": "n.249-13090T>G",
"hgvs_p": null,
"transcript": "ENST00000439077.1",
"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": 514,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000439077.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CHMP3-AS1",
"gene_hgnc_id": 55795,
"hgvs_c": "n.645-13090T>G",
"hgvs_p": null,
"transcript": "ENST00000597638.1",
"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": 818,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000597638.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CHMP3-AS1",
"gene_hgnc_id": 55795,
"hgvs_c": "n.223-13090T>G",
"hgvs_p": null,
"transcript": "ENST00000725269.1",
"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": 488,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000725269.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CHMP3-AS1",
"gene_hgnc_id": 55795,
"hgvs_c": "n.254-13090T>G",
"hgvs_p": null,
"transcript": "NR_183900.1",
"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": 527,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_183900.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "CHMP3-AS1",
"gene_hgnc_id": 55795,
"hgvs_c": "n.645-13090T>G",
"hgvs_p": null,
"transcript": "NR_183901.1",
"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": 918,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_183901.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHMP3-AS1",
"gene_hgnc_id": 55795,
"hgvs_c": "n.-204T>G",
"hgvs_p": null,
"transcript": "ENST00000424788.1",
"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": 1147,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000424788.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"hgvs_c": "n.*234A>C",
"hgvs_p": null,
"transcript": "ENST00000463333.6",
"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": 686,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000463333.6"
}
],
"gene_symbol": "RNF103",
"gene_hgnc_id": 12859,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.09028109908103943,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.136,
"revel_prediction": "Benign",
"alphamissense_score": 0.1241,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.222,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_005667.4",
"gene_symbol": "RNF103",
"hgnc_id": 12859,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1815A>C",
"hgvs_p": "p.Glu605Asp"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001198954.1",
"gene_symbol": "RNF103-CHMP3",
"hgnc_id": 38847,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.132+16244A>C",
"hgvs_p": null
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000426549.1",
"gene_symbol": "CHMP3-AS1",
"hgnc_id": 55795,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.80T>G",
"hgvs_p": null
}
],
"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
}