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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-77654205-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=77654205&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 77654205,
"ref": "C",
"alt": "T",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000373344.11",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.4215-5G>A",
"hgvs_p": null,
"transcript": "NM_000489.6",
"protein_id": "NP_000480.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2492,
"cds_start": -4,
"cds_end": null,
"cds_length": 7479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11165,
"mane_select": "ENST00000373344.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.4215-5G>A",
"hgvs_p": null,
"transcript": "ENST00000373344.11",
"protein_id": "ENSP00000362441.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 2492,
"cds_start": -4,
"cds_end": null,
"cds_length": 7479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11165,
"mane_select": "NM_000489.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.4101-5G>A",
"hgvs_p": null,
"transcript": "ENST00000395603.7",
"protein_id": "ENSP00000378967.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 2454,
"cds_start": -4,
"cds_end": null,
"cds_length": 7365,
"cdna_start": null,
"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": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.4011-5G>A",
"hgvs_p": null,
"transcript": "ENST00000624166.3",
"protein_id": "ENSP00000485103.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1350,
"cds_start": -4,
"cds_end": null,
"cds_length": 4053,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4272,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "n.*3843-5G>A",
"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": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.4101-5G>A",
"hgvs_p": null,
"transcript": "NM_138270.5",
"protein_id": "NP_612114.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2454,
"cds_start": -4,
"cds_end": null,
"cds_length": 7365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.4212-5G>A",
"hgvs_p": null,
"transcript": "XM_005262153.6",
"protein_id": "XP_005262210.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2491,
"cds_start": -4,
"cds_end": null,
"cds_length": 7476,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11162,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.4128-5G>A",
"hgvs_p": null,
"transcript": "XM_005262154.6",
"protein_id": "XP_005262211.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2463,
"cds_start": -4,
"cds_end": null,
"cds_length": 7392,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11078,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.4125-5G>A",
"hgvs_p": null,
"transcript": "XM_017029601.3",
"protein_id": "XP_016885090.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2462,
"cds_start": -4,
"cds_end": null,
"cds_length": 7389,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11075,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.4098-5G>A",
"hgvs_p": null,
"transcript": "XM_006724666.5",
"protein_id": "XP_006724729.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2453,
"cds_start": -4,
"cds_end": null,
"cds_length": 7362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11048,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.4050-5G>A",
"hgvs_p": null,
"transcript": "XM_005262156.5",
"protein_id": "XP_005262213.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2437,
"cds_start": -4,
"cds_end": null,
"cds_length": 7314,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11052,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.4014-5G>A",
"hgvs_p": null,
"transcript": "XM_017029604.3",
"protein_id": "XP_016885093.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2425,
"cds_start": -4,
"cds_end": null,
"cds_length": 7278,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10964,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.4011-5G>A",
"hgvs_p": null,
"transcript": "XM_005262157.6",
"protein_id": "XP_005262214.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2424,
"cds_start": -4,
"cds_end": null,
"cds_length": 7275,
"cdna_start": null,
"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": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.4215-5G>A",
"hgvs_p": null,
"transcript": "XM_047442191.1",
"protein_id": "XP_047298147.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2038,
"cds_start": -4,
"cds_end": null,
"cds_length": 6117,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"hgvs_c": "c.4215-5G>A",
"hgvs_p": null,
"transcript": "XM_006724668.4",
"protein_id": "XP_006724731.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1871,
"cds_start": -4,
"cds_end": null,
"cds_length": 5616,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"dbsnp": "rs111833322",
"frequency_reference_population": 0.0001594459,
"hom_count_reference_population": 58,
"allele_count_reference_population": 189,
"gnomad_exomes_af": 0.000157392,
"gnomad_genomes_af": 0.000179208,
"gnomad_exomes_ac": 169,
"gnomad_genomes_ac": 20,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.28999999165534973,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.04800000041723251,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.064,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000103593264399914,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -18,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -18,
"benign_score": 18,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000373344.11",
"gene_symbol": "ATRX",
"hgnc_id": 886,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.4215-5G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Alpha thalassemia-X-linked intellectual disability syndrome,Inborn genetic diseases,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:2",
"phenotype_combined": "Alpha thalassemia-X-linked intellectual disability syndrome|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}