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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: X-77520832-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=77520832&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 77520832,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000373344.11",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.7156C>T",
"hgvs_p": "p.Arg2386*",
"transcript": "NM_000489.6",
"protein_id": "NP_000480.3",
"transcript_support_level": null,
"aa_start": 2386,
"aa_end": null,
"aa_length": 2492,
"cds_start": 7156,
"cds_end": null,
"cds_length": 7479,
"cdna_start": 7371,
"cdna_end": null,
"cdna_length": 11165,
"mane_select": "ENST00000373344.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.7156C>T",
"hgvs_p": "p.Arg2386*",
"transcript": "ENST00000373344.11",
"protein_id": "ENSP00000362441.4",
"transcript_support_level": 1,
"aa_start": 2386,
"aa_end": null,
"aa_length": 2492,
"cds_start": 7156,
"cds_end": null,
"cds_length": 7479,
"cdna_start": 7371,
"cdna_end": null,
"cdna_length": 11165,
"mane_select": "NM_000489.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.7042C>T",
"hgvs_p": "p.Arg2348*",
"transcript": "ENST00000395603.7",
"protein_id": "ENSP00000378967.3",
"transcript_support_level": 1,
"aa_start": 2348,
"aa_end": null,
"aa_length": 2454,
"cds_start": 7042,
"cds_end": null,
"cds_length": 7365,
"cdna_start": 7257,
"cdna_end": null,
"cdna_length": 10218,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "n.*6784C>T",
"hgvs_p": null,
"transcript": "ENST00000480283.5",
"protein_id": "ENSP00000480196.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "n.*6784C>T",
"hgvs_p": null,
"transcript": "ENST00000480283.5",
"protein_id": "ENSP00000480196.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.7042C>T",
"hgvs_p": "p.Arg2348*",
"transcript": "NM_138270.5",
"protein_id": "NP_612114.2",
"transcript_support_level": null,
"aa_start": 2348,
"aa_end": null,
"aa_length": 2454,
"cds_start": 7042,
"cds_end": null,
"cds_length": 7365,
"cdna_start": 7257,
"cdna_end": null,
"cdna_length": 11051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.2254C>T",
"hgvs_p": "p.Arg752*",
"transcript": "ENST00000675732.1",
"protein_id": "ENSP00000502598.1",
"transcript_support_level": null,
"aa_start": 752,
"aa_end": null,
"aa_length": 858,
"cds_start": 2254,
"cds_end": null,
"cds_length": 2577,
"cdna_start": 2886,
"cdna_end": null,
"cdna_length": 5847,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.7153C>T",
"hgvs_p": "p.Arg2385*",
"transcript": "XM_005262153.6",
"protein_id": "XP_005262210.2",
"transcript_support_level": null,
"aa_start": 2385,
"aa_end": null,
"aa_length": 2491,
"cds_start": 7153,
"cds_end": null,
"cds_length": 7476,
"cdna_start": 7368,
"cdna_end": null,
"cdna_length": 11162,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.7069C>T",
"hgvs_p": "p.Arg2357*",
"transcript": "XM_005262154.6",
"protein_id": "XP_005262211.2",
"transcript_support_level": null,
"aa_start": 2357,
"aa_end": null,
"aa_length": 2463,
"cds_start": 7069,
"cds_end": null,
"cds_length": 7392,
"cdna_start": 7284,
"cdna_end": null,
"cdna_length": 11078,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.7066C>T",
"hgvs_p": "p.Arg2356*",
"transcript": "XM_017029601.3",
"protein_id": "XP_016885090.1",
"transcript_support_level": null,
"aa_start": 2356,
"aa_end": null,
"aa_length": 2462,
"cds_start": 7066,
"cds_end": null,
"cds_length": 7389,
"cdna_start": 7281,
"cdna_end": null,
"cdna_length": 11075,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.7039C>T",
"hgvs_p": "p.Arg2347*",
"transcript": "XM_006724666.5",
"protein_id": "XP_006724729.1",
"transcript_support_level": null,
"aa_start": 2347,
"aa_end": null,
"aa_length": 2453,
"cds_start": 7039,
"cds_end": null,
"cds_length": 7362,
"cdna_start": 7254,
"cdna_end": null,
"cdna_length": 11048,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.6991C>T",
"hgvs_p": "p.Arg2331*",
"transcript": "XM_005262156.5",
"protein_id": "XP_005262213.2",
"transcript_support_level": null,
"aa_start": 2331,
"aa_end": null,
"aa_length": 2437,
"cds_start": 6991,
"cds_end": null,
"cds_length": 7314,
"cdna_start": 7258,
"cdna_end": null,
"cdna_length": 11052,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.6955C>T",
"hgvs_p": "p.Arg2319*",
"transcript": "XM_017029604.3",
"protein_id": "XP_016885093.1",
"transcript_support_level": null,
"aa_start": 2319,
"aa_end": null,
"aa_length": 2425,
"cds_start": 6955,
"cds_end": null,
"cds_length": 7278,
"cdna_start": 7170,
"cdna_end": null,
"cdna_length": 10964,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.6952C>T",
"hgvs_p": "p.Arg2318*",
"transcript": "XM_005262157.6",
"protein_id": "XP_005262214.2",
"transcript_support_level": null,
"aa_start": 2318,
"aa_end": null,
"aa_length": 2424,
"cds_start": 6952,
"cds_end": null,
"cds_length": 7275,
"cdna_start": 7167,
"cdna_end": null,
"cdna_length": 10961,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "n.5476C>T",
"hgvs_p": null,
"transcript": "ENST00000623706.3",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7245,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "n.387C>T",
"hgvs_p": null,
"transcript": "ENST00000624766.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 580,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "n.*204C>T",
"hgvs_p": null,
"transcript": "ENST00000637959.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 86,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"dbsnp": "rs122445099",
"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": 0.5799999833106995,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.58,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.901,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.04,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000373344.11",
"gene_symbol": "ATRX",
"hgnc_id": 886,
"effects": [
"stop_gained"
],
"inheritance_mode": "XL",
"hgvs_c": "c.7156C>T",
"hgvs_p": "p.Arg2386*"
}
],
"clinvar_disease": " 1, X-linked,ATRX-related disorder,Alpha thalassemia-X-linked intellectual disability syndrome,Intellectual disability-hypotonic facies syndrome,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:6",
"phenotype_combined": "Alpha thalassemia-X-linked intellectual disability syndrome|not provided|Intellectual disability-hypotonic facies syndrome, X-linked, 1|ATRX-related disorder",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}