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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: 2-135130060-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=135130060&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"stop_gained"
],
"gene_symbol": "RAB3GAP1",
"hgnc_id": 17063,
"hgvs_c": "c.1039C>T",
"hgvs_p": "p.Arg347*",
"inheritance_mode": "AR",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_001172435.2",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 33,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.63,
"chr": "2",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Inborn genetic diseases,Martsolf syndrome 2,Warburg micro syndrome 1,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5 O:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.6299999952316284,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 981,
"aa_ref": "R",
"aa_start": 347,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4891,
"cdna_start": 1055,
"cds_end": null,
"cds_length": 2946,
"cds_start": 1039,
"consequences": [
"stop_gained"
],
"exon_count": 24,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_012233.3",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "c.1039C>T",
"hgvs_p": "p.Arg347*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000264158.13",
"protein_coding": true,
"protein_id": "NP_036365.1",
"strand": true,
"transcript": "NM_012233.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 981,
"aa_ref": "R",
"aa_start": 347,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4891,
"cdna_start": 1055,
"cds_end": null,
"cds_length": 2946,
"cds_start": 1039,
"consequences": [
"stop_gained"
],
"exon_count": 24,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000264158.13",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "c.1039C>T",
"hgvs_p": "p.Arg347*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_012233.3",
"protein_coding": true,
"protein_id": "ENSP00000264158.8",
"strand": true,
"transcript": "ENST00000264158.13",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 988,
"aa_ref": "R",
"aa_start": 347,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4185,
"cdna_start": 1049,
"cds_end": null,
"cds_length": 2967,
"cds_start": 1039,
"consequences": [
"stop_gained"
],
"exon_count": 25,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000442034.5",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "c.1039C>T",
"hgvs_p": "p.Arg347*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000411418.1",
"strand": true,
"transcript": "ENST00000442034.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 642,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2292,
"cdna_start": null,
"cds_end": null,
"cds_length": 1929,
"cds_start": null,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_count": 15,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_047443732.1",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "c.-108C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047299688.1",
"strand": true,
"transcript": "XM_047443732.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 988,
"aa_ref": "R",
"aa_start": 347,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4912,
"cdna_start": 1055,
"cds_end": null,
"cds_length": 2967,
"cds_start": 1039,
"consequences": [
"stop_gained"
],
"exon_count": 25,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_001172435.2",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "c.1039C>T",
"hgvs_p": "p.Arg347*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001165906.1",
"strand": true,
"transcript": "NM_001172435.2",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 982,
"aa_ref": "R",
"aa_start": 348,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3398,
"cdna_start": 1063,
"cds_end": null,
"cds_length": 2949,
"cds_start": 1042,
"consequences": [
"stop_gained"
],
"exon_count": 24,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000970735.1",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "c.1042C>T",
"hgvs_p": "p.Arg348*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000640794.1",
"strand": true,
"transcript": "ENST00000970735.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 979,
"aa_ref": "R",
"aa_start": 345,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3611,
"cdna_start": 1046,
"cds_end": null,
"cds_length": 2940,
"cds_start": 1033,
"consequences": [
"stop_gained"
],
"exon_count": 24,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000855137.1",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "c.1033C>T",
"hgvs_p": "p.Arg345*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000525196.1",
"strand": true,
"transcript": "ENST00000855137.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 973,
"aa_ref": "R",
"aa_start": 347,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4155,
"cdna_start": 1064,
"cds_end": null,
"cds_length": 2922,
"cds_start": 1039,
"consequences": [
"stop_gained"
],
"exon_count": 24,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000855134.1",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "c.1039C>T",
"hgvs_p": "p.Arg347*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000525193.1",
"strand": true,
"transcript": "ENST00000855134.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 914,
"aa_ref": "R",
"aa_start": 347,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3950,
"cdna_start": 1052,
"cds_end": null,
"cds_length": 2745,
"cds_start": 1039,
"consequences": [
"stop_gained"
],
"exon_count": 22,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000855136.1",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "c.1039C>T",
"hgvs_p": "p.Arg347*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000525195.1",
"strand": true,
"transcript": "ENST00000855136.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 815,
"aa_ref": "R",
"aa_start": 181,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3669,
"cdna_start": 554,
"cds_end": null,
"cds_length": 2448,
"cds_start": 541,
"consequences": [
"stop_gained"
],
"exon_count": 20,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000855135.1",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "c.541C>T",
"hgvs_p": "p.Arg181*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000525194.1",
"strand": true,
"transcript": "ENST00000855135.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 1024,
"aa_ref": "R",
"aa_start": 347,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3220,
"cdna_start": 1055,
"cds_end": null,
"cds_length": 3075,
"cds_start": 1039,
"consequences": [
"stop_gained"
],
"exon_count": 25,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "XM_011510823.4",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "c.1039C>T",
"hgvs_p": "p.Arg347*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011509125.1",
"strand": true,
"transcript": "XM_011510823.4",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 979,
"aa_ref": "R",
"aa_start": 347,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3485,
"cdna_start": 1055,
"cds_end": null,
"cds_length": 2940,
"cds_start": 1039,
"consequences": [
"stop_gained"
],
"exon_count": 25,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "XM_011510825.4",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "c.1039C>T",
"hgvs_p": "p.Arg347*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011509127.1",
"strand": true,
"transcript": "XM_011510825.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 642,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2292,
"cdna_start": null,
"cds_end": null,
"cds_length": 1929,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 15,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_047443732.1",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "c.-108C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047299688.1",
"strand": true,
"transcript": "XM_047443732.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 135,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1708,
"cdna_start": null,
"cds_end": null,
"cds_length": 408,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000688182.1",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "c.151-37633C>T",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509324.1",
"strand": true,
"transcript": "ENST00000688182.1",
"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": 3506,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 25,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000487003.5",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "n.1108C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000487003.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 557,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000489858.1",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "n.376C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000489858.1",
"transcript_support_level": 2
},
{
"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": 3614,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 26,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000539493.3",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "n.1039C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000444306.2",
"strand": true,
"transcript": "ENST00000539493.3",
"transcript_support_level": 5
},
{
"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": 4344,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 21,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000685967.1",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "n.*496C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000508423.1",
"strand": true,
"transcript": "ENST00000685967.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3935,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 18,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000686114.1",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "n.1385C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000686114.1",
"transcript_support_level": null
},
{
"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": 5136,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 26,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000687199.1",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
"hgvs_c": "n.*1107C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000510319.1",
"strand": true,
"transcript": "ENST00000687199.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 8038,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 24,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000688088.1",
"gene_hgnc_id": 17063,
"gene_symbol": "RAB3GAP1",
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"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "Warburg micro syndrome 1|not provided|Warburg micro syndrome 1;Martsolf syndrome 2|Inborn genetic diseases",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.304,
"pos": 135130060,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001172435.2"
}
]
}