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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-77681715-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=77681715&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 77681715,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000373344.11",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "L",
"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.3541G>C",
"hgvs_p": "p.Val1181Leu",
"transcript": "NM_000489.6",
"protein_id": "NP_000480.3",
"transcript_support_level": null,
"aa_start": 1181,
"aa_end": null,
"aa_length": 2492,
"cds_start": 3541,
"cds_end": null,
"cds_length": 7479,
"cdna_start": 3756,
"cdna_end": null,
"cdna_length": 11165,
"mane_select": "ENST00000373344.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"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.3541G>C",
"hgvs_p": "p.Val1181Leu",
"transcript": "ENST00000373344.11",
"protein_id": "ENSP00000362441.4",
"transcript_support_level": 1,
"aa_start": 1181,
"aa_end": null,
"aa_length": 2492,
"cds_start": 3541,
"cds_end": null,
"cds_length": 7479,
"cdna_start": 3756,
"cdna_end": null,
"cdna_length": 11165,
"mane_select": "NM_000489.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"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.3427G>C",
"hgvs_p": "p.Val1143Leu",
"transcript": "ENST00000395603.7",
"protein_id": "ENSP00000378967.3",
"transcript_support_level": 1,
"aa_start": 1143,
"aa_end": null,
"aa_length": 2454,
"cds_start": 3427,
"cds_end": null,
"cds_length": 7365,
"cdna_start": 3642,
"cdna_end": null,
"cdna_length": 10218,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"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.3337G>C",
"hgvs_p": "p.Val1113Leu",
"transcript": "ENST00000624166.3",
"protein_id": "ENSP00000485103.1",
"transcript_support_level": 1,
"aa_start": 1113,
"aa_end": null,
"aa_length": 1350,
"cds_start": 3337,
"cds_end": null,
"cds_length": 4053,
"cdna_start": 3556,
"cdna_end": null,
"cdna_length": 4272,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.427G>C",
"hgvs_p": "p.Val143Leu",
"transcript": "ENST00000493470.2",
"protein_id": "ENSP00000485408.1",
"transcript_support_level": 1,
"aa_start": 143,
"aa_end": null,
"aa_length": 293,
"cds_start": 427,
"cds_end": null,
"cds_length": 882,
"cdna_start": 427,
"cdna_end": null,
"cdna_length": 2967,
"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.*3169G>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.*3169G>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": "V",
"aa_alt": "L",
"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.3427G>C",
"hgvs_p": "p.Val1143Leu",
"transcript": "NM_138270.5",
"protein_id": "NP_612114.2",
"transcript_support_level": null,
"aa_start": 1143,
"aa_end": null,
"aa_length": 2454,
"cds_start": 3427,
"cds_end": null,
"cds_length": 7365,
"cdna_start": 3642,
"cdna_end": null,
"cdna_length": 11051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"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.3538G>C",
"hgvs_p": "p.Val1180Leu",
"transcript": "XM_005262153.6",
"protein_id": "XP_005262210.2",
"transcript_support_level": null,
"aa_start": 1180,
"aa_end": null,
"aa_length": 2491,
"cds_start": 3538,
"cds_end": null,
"cds_length": 7476,
"cdna_start": 3753,
"cdna_end": null,
"cdna_length": 11162,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"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.3454G>C",
"hgvs_p": "p.Val1152Leu",
"transcript": "XM_005262154.6",
"protein_id": "XP_005262211.2",
"transcript_support_level": null,
"aa_start": 1152,
"aa_end": null,
"aa_length": 2463,
"cds_start": 3454,
"cds_end": null,
"cds_length": 7392,
"cdna_start": 3669,
"cdna_end": null,
"cdna_length": 11078,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"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.3451G>C",
"hgvs_p": "p.Val1151Leu",
"transcript": "XM_017029601.3",
"protein_id": "XP_016885090.1",
"transcript_support_level": null,
"aa_start": 1151,
"aa_end": null,
"aa_length": 2462,
"cds_start": 3451,
"cds_end": null,
"cds_length": 7389,
"cdna_start": 3666,
"cdna_end": null,
"cdna_length": 11075,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"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.3424G>C",
"hgvs_p": "p.Val1142Leu",
"transcript": "XM_006724666.5",
"protein_id": "XP_006724729.1",
"transcript_support_level": null,
"aa_start": 1142,
"aa_end": null,
"aa_length": 2453,
"cds_start": 3424,
"cds_end": null,
"cds_length": 7362,
"cdna_start": 3639,
"cdna_end": null,
"cdna_length": 11048,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"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.3376G>C",
"hgvs_p": "p.Val1126Leu",
"transcript": "XM_005262156.5",
"protein_id": "XP_005262213.2",
"transcript_support_level": null,
"aa_start": 1126,
"aa_end": null,
"aa_length": 2437,
"cds_start": 3376,
"cds_end": null,
"cds_length": 7314,
"cdna_start": 3643,
"cdna_end": null,
"cdna_length": 11052,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"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.3340G>C",
"hgvs_p": "p.Val1114Leu",
"transcript": "XM_017029604.3",
"protein_id": "XP_016885093.1",
"transcript_support_level": null,
"aa_start": 1114,
"aa_end": null,
"aa_length": 2425,
"cds_start": 3340,
"cds_end": null,
"cds_length": 7278,
"cdna_start": 3555,
"cdna_end": null,
"cdna_length": 10964,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"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.3337G>C",
"hgvs_p": "p.Val1113Leu",
"transcript": "XM_005262157.6",
"protein_id": "XP_005262214.2",
"transcript_support_level": null,
"aa_start": 1113,
"aa_end": null,
"aa_length": 2424,
"cds_start": 3337,
"cds_end": null,
"cds_length": 7275,
"cdna_start": 3552,
"cdna_end": null,
"cdna_length": 10961,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"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.3541G>C",
"hgvs_p": "p.Val1181Leu",
"transcript": "XM_047442191.1",
"protein_id": "XP_047298147.1",
"transcript_support_level": null,
"aa_start": 1181,
"aa_end": null,
"aa_length": 2038,
"cds_start": 3541,
"cds_end": null,
"cds_length": 6117,
"cdna_start": 3756,
"cdna_end": null,
"cdna_length": 6398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "L",
"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.3541G>C",
"hgvs_p": "p.Val1181Leu",
"transcript": "XM_006724668.4",
"protein_id": "XP_006724731.1",
"transcript_support_level": null,
"aa_start": 1181,
"aa_end": null,
"aa_length": 1871,
"cds_start": 3541,
"cds_end": null,
"cds_length": 5616,
"cdna_start": 3756,
"cdna_end": null,
"cdna_length": 6044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"dbsnp": "rs61758732",
"frequency_reference_population": 0.0012890232,
"hom_count_reference_population": 522,
"allele_count_reference_population": 1554,
"gnomad_exomes_af": 0.00128682,
"gnomad_genomes_af": 0.00131064,
"gnomad_exomes_ac": 1408,
"gnomad_genomes_ac": 146,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.006064116954803467,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.12,
"revel_prediction": "Benign",
"alphamissense_score": 0.1122,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.798,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000373344.11",
"gene_symbol": "ATRX",
"hgnc_id": 886,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.3541G>C",
"hgvs_p": "p.Val1181Leu"
}
],
"clinvar_disease": "ATRX-related disorder,Alpha thalassemia-X-linked intellectual disability syndrome,Inborn genetic diseases,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4 O:1",
"phenotype_combined": "not specified|Alpha thalassemia-X-linked intellectual disability syndrome|not provided|Inborn genetic diseases|ATRX-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}