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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-77682471-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=77682471&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 77682471,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000373344.11",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.2785G>C",
"hgvs_p": "p.Glu929Gln",
"transcript": "NM_000489.6",
"protein_id": "NP_000480.3",
"transcript_support_level": null,
"aa_start": 929,
"aa_end": null,
"aa_length": 2492,
"cds_start": 2785,
"cds_end": null,
"cds_length": 7479,
"cdna_start": 3000,
"cdna_end": null,
"cdna_length": 11165,
"mane_select": "ENST00000373344.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.2785G>C",
"hgvs_p": "p.Glu929Gln",
"transcript": "ENST00000373344.11",
"protein_id": "ENSP00000362441.4",
"transcript_support_level": 1,
"aa_start": 929,
"aa_end": null,
"aa_length": 2492,
"cds_start": 2785,
"cds_end": null,
"cds_length": 7479,
"cdna_start": 3000,
"cdna_end": null,
"cdna_length": 11165,
"mane_select": "NM_000489.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.2671G>C",
"hgvs_p": "p.Glu891Gln",
"transcript": "ENST00000395603.7",
"protein_id": "ENSP00000378967.3",
"transcript_support_level": 1,
"aa_start": 891,
"aa_end": null,
"aa_length": 2454,
"cds_start": 2671,
"cds_end": null,
"cds_length": 7365,
"cdna_start": 2886,
"cdna_end": null,
"cdna_length": 10218,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.2581G>C",
"hgvs_p": "p.Glu861Gln",
"transcript": "ENST00000624166.3",
"protein_id": "ENSP00000485103.1",
"transcript_support_level": 1,
"aa_start": 861,
"aa_end": null,
"aa_length": 1350,
"cds_start": 2581,
"cds_end": null,
"cds_length": 4053,
"cdna_start": 2800,
"cdna_end": null,
"cdna_length": 4272,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.2698G>C",
"hgvs_p": "p.Glu900Gln",
"transcript": "ENST00000624032.3",
"protein_id": "ENSP00000485253.1",
"transcript_support_level": 1,
"aa_start": 900,
"aa_end": null,
"aa_length": 953,
"cds_start": 2698,
"cds_end": null,
"cds_length": 2864,
"cdna_start": 2905,
"cdna_end": null,
"cdna_length": 3071,
"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": 10,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "n.*2413G>C",
"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": 10,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "n.*2413G>C",
"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": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.2671G>C",
"hgvs_p": "p.Glu891Gln",
"transcript": "NM_138270.5",
"protein_id": "NP_612114.2",
"transcript_support_level": null,
"aa_start": 891,
"aa_end": null,
"aa_length": 2454,
"cds_start": 2671,
"cds_end": null,
"cds_length": 7365,
"cdna_start": 2886,
"cdna_end": null,
"cdna_length": 11051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.2782G>C",
"hgvs_p": "p.Glu928Gln",
"transcript": "XM_005262153.6",
"protein_id": "XP_005262210.2",
"transcript_support_level": null,
"aa_start": 928,
"aa_end": null,
"aa_length": 2491,
"cds_start": 2782,
"cds_end": null,
"cds_length": 7476,
"cdna_start": 2997,
"cdna_end": null,
"cdna_length": 11162,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.2698G>C",
"hgvs_p": "p.Glu900Gln",
"transcript": "XM_005262154.6",
"protein_id": "XP_005262211.2",
"transcript_support_level": null,
"aa_start": 900,
"aa_end": null,
"aa_length": 2463,
"cds_start": 2698,
"cds_end": null,
"cds_length": 7392,
"cdna_start": 2913,
"cdna_end": null,
"cdna_length": 11078,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.2695G>C",
"hgvs_p": "p.Glu899Gln",
"transcript": "XM_017029601.3",
"protein_id": "XP_016885090.1",
"transcript_support_level": null,
"aa_start": 899,
"aa_end": null,
"aa_length": 2462,
"cds_start": 2695,
"cds_end": null,
"cds_length": 7389,
"cdna_start": 2910,
"cdna_end": null,
"cdna_length": 11075,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.2668G>C",
"hgvs_p": "p.Glu890Gln",
"transcript": "XM_006724666.5",
"protein_id": "XP_006724729.1",
"transcript_support_level": null,
"aa_start": 890,
"aa_end": null,
"aa_length": 2453,
"cds_start": 2668,
"cds_end": null,
"cds_length": 7362,
"cdna_start": 2883,
"cdna_end": null,
"cdna_length": 11048,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.2620G>C",
"hgvs_p": "p.Glu874Gln",
"transcript": "XM_005262156.5",
"protein_id": "XP_005262213.2",
"transcript_support_level": null,
"aa_start": 874,
"aa_end": null,
"aa_length": 2437,
"cds_start": 2620,
"cds_end": null,
"cds_length": 7314,
"cdna_start": 2887,
"cdna_end": null,
"cdna_length": 11052,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.2584G>C",
"hgvs_p": "p.Glu862Gln",
"transcript": "XM_017029604.3",
"protein_id": "XP_016885093.1",
"transcript_support_level": null,
"aa_start": 862,
"aa_end": null,
"aa_length": 2425,
"cds_start": 2584,
"cds_end": null,
"cds_length": 7278,
"cdna_start": 2799,
"cdna_end": null,
"cdna_length": 10964,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.2581G>C",
"hgvs_p": "p.Glu861Gln",
"transcript": "XM_005262157.6",
"protein_id": "XP_005262214.2",
"transcript_support_level": null,
"aa_start": 861,
"aa_end": null,
"aa_length": 2424,
"cds_start": 2581,
"cds_end": null,
"cds_length": 7275,
"cdna_start": 2796,
"cdna_end": null,
"cdna_length": 10961,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.2785G>C",
"hgvs_p": "p.Glu929Gln",
"transcript": "XM_047442191.1",
"protein_id": "XP_047298147.1",
"transcript_support_level": null,
"aa_start": 929,
"aa_end": null,
"aa_length": 2038,
"cds_start": 2785,
"cds_end": null,
"cds_length": 6117,
"cdna_start": 3000,
"cdna_end": null,
"cdna_length": 6398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.2785G>C",
"hgvs_p": "p.Glu929Gln",
"transcript": "XM_006724668.4",
"protein_id": "XP_006724731.1",
"transcript_support_level": null,
"aa_start": 929,
"aa_end": null,
"aa_length": 1871,
"cds_start": 2785,
"cds_end": null,
"cds_length": 5616,
"cdna_start": 3000,
"cdna_end": null,
"cdna_length": 6044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"dbsnp": "rs3088074",
"frequency_reference_population": 0.51583225,
"hom_count_reference_population": 29550,
"allele_count_reference_population": 56903,
"gnomad_exomes_af": 0.668884,
"gnomad_genomes_af": 0.515832,
"gnomad_exomes_ac": 734383,
"gnomad_genomes_ac": 56903,
"gnomad_exomes_homalt": 169861,
"gnomad_genomes_homalt": 12893,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.006577014923095703,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": 0.108,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.93,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.28,
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BA1",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000373344.11",
"gene_symbol": "ATRX",
"hgnc_id": 886,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.2785G>C",
"hgvs_p": "p.Glu929Gln"
}
],
"clinvar_disease": "Alpha thalassemia-X-linked intellectual disability syndrome",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "Alpha thalassemia-X-linked intellectual disability syndrome",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}