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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-77683006-TGAA-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=77683006&ref=TGAA&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 77683006,
"ref": "TGAA",
"alt": "T",
"effect": "disruptive_inframe_deletion",
"transcript": "ENST00000373344.11",
"consequences": [
{
"aa_ref": "SS",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"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.2247_2249delTTC",
"hgvs_p": "p.Ser750del",
"transcript": "NM_000489.6",
"protein_id": "NP_000480.3",
"transcript_support_level": null,
"aa_start": 749,
"aa_end": null,
"aa_length": 2492,
"cds_start": 2247,
"cds_end": null,
"cds_length": 7479,
"cdna_start": 2464,
"cdna_end": null,
"cdna_length": 11165,
"mane_select": "ENST00000373344.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SS",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"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.2247_2249delTTC",
"hgvs_p": "p.Ser750del",
"transcript": "ENST00000373344.11",
"protein_id": "ENSP00000362441.4",
"transcript_support_level": 1,
"aa_start": 749,
"aa_end": null,
"aa_length": 2492,
"cds_start": 2247,
"cds_end": null,
"cds_length": 7479,
"cdna_start": 2464,
"cdna_end": null,
"cdna_length": 11165,
"mane_select": "NM_000489.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SS",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"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.2133_2135delTTC",
"hgvs_p": "p.Ser712del",
"transcript": "ENST00000395603.7",
"protein_id": "ENSP00000378967.3",
"transcript_support_level": 1,
"aa_start": 711,
"aa_end": null,
"aa_length": 2454,
"cds_start": 2133,
"cds_end": null,
"cds_length": 7365,
"cdna_start": 2350,
"cdna_end": null,
"cdna_length": 10218,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SS",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"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.2043_2045delTTC",
"hgvs_p": "p.Ser682del",
"transcript": "ENST00000624166.3",
"protein_id": "ENSP00000485103.1",
"transcript_support_level": 1,
"aa_start": 681,
"aa_end": null,
"aa_length": 1350,
"cds_start": 2043,
"cds_end": null,
"cds_length": 4053,
"cdna_start": 2264,
"cdna_end": null,
"cdna_length": 4272,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SS",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"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.2160_2162delTTC",
"hgvs_p": "p.Ser721del",
"transcript": "ENST00000624032.3",
"protein_id": "ENSP00000485253.1",
"transcript_support_level": 1,
"aa_start": 720,
"aa_end": null,
"aa_length": 953,
"cds_start": 2160,
"cds_end": null,
"cds_length": 2864,
"cdna_start": 2369,
"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.*1875_*1877delTTC",
"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.*1875_*1877delTTC",
"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": "SS",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"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.2133_2135delTTC",
"hgvs_p": "p.Ser712del",
"transcript": "NM_138270.5",
"protein_id": "NP_612114.2",
"transcript_support_level": null,
"aa_start": 711,
"aa_end": null,
"aa_length": 2454,
"cds_start": 2133,
"cds_end": null,
"cds_length": 7365,
"cdna_start": 2350,
"cdna_end": null,
"cdna_length": 11051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SS",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"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.2244_2246delTTC",
"hgvs_p": "p.Ser749del",
"transcript": "XM_005262153.6",
"protein_id": "XP_005262210.2",
"transcript_support_level": null,
"aa_start": 748,
"aa_end": null,
"aa_length": 2491,
"cds_start": 2244,
"cds_end": null,
"cds_length": 7476,
"cdna_start": 2461,
"cdna_end": null,
"cdna_length": 11162,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SS",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"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.2160_2162delTTC",
"hgvs_p": "p.Ser721del",
"transcript": "XM_005262154.6",
"protein_id": "XP_005262211.2",
"transcript_support_level": null,
"aa_start": 720,
"aa_end": null,
"aa_length": 2463,
"cds_start": 2160,
"cds_end": null,
"cds_length": 7392,
"cdna_start": 2377,
"cdna_end": null,
"cdna_length": 11078,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SS",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"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.2157_2159delTTC",
"hgvs_p": "p.Ser720del",
"transcript": "XM_017029601.3",
"protein_id": "XP_016885090.1",
"transcript_support_level": null,
"aa_start": 719,
"aa_end": null,
"aa_length": 2462,
"cds_start": 2157,
"cds_end": null,
"cds_length": 7389,
"cdna_start": 2374,
"cdna_end": null,
"cdna_length": 11075,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SS",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"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.2130_2132delTTC",
"hgvs_p": "p.Ser711del",
"transcript": "XM_006724666.5",
"protein_id": "XP_006724729.1",
"transcript_support_level": null,
"aa_start": 710,
"aa_end": null,
"aa_length": 2453,
"cds_start": 2130,
"cds_end": null,
"cds_length": 7362,
"cdna_start": 2347,
"cdna_end": null,
"cdna_length": 11048,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SS",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"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.2082_2084delTTC",
"hgvs_p": "p.Ser695del",
"transcript": "XM_005262156.5",
"protein_id": "XP_005262213.2",
"transcript_support_level": null,
"aa_start": 694,
"aa_end": null,
"aa_length": 2437,
"cds_start": 2082,
"cds_end": null,
"cds_length": 7314,
"cdna_start": 2351,
"cdna_end": null,
"cdna_length": 11052,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SS",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"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.2046_2048delTTC",
"hgvs_p": "p.Ser683del",
"transcript": "XM_017029604.3",
"protein_id": "XP_016885093.1",
"transcript_support_level": null,
"aa_start": 682,
"aa_end": null,
"aa_length": 2425,
"cds_start": 2046,
"cds_end": null,
"cds_length": 7278,
"cdna_start": 2263,
"cdna_end": null,
"cdna_length": 10964,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SS",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"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.2043_2045delTTC",
"hgvs_p": "p.Ser682del",
"transcript": "XM_005262157.6",
"protein_id": "XP_005262214.2",
"transcript_support_level": null,
"aa_start": 681,
"aa_end": null,
"aa_length": 2424,
"cds_start": 2043,
"cds_end": null,
"cds_length": 7275,
"cdna_start": 2260,
"cdna_end": null,
"cdna_length": 10961,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SS",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"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.2247_2249delTTC",
"hgvs_p": "p.Ser750del",
"transcript": "XM_047442191.1",
"protein_id": "XP_047298147.1",
"transcript_support_level": null,
"aa_start": 749,
"aa_end": null,
"aa_length": 2038,
"cds_start": 2247,
"cds_end": null,
"cds_length": 6117,
"cdna_start": 2464,
"cdna_end": null,
"cdna_length": 6398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "SS",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"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.2247_2249delTTC",
"hgvs_p": "p.Ser750del",
"transcript": "XM_006724668.4",
"protein_id": "XP_006724731.1",
"transcript_support_level": null,
"aa_start": 749,
"aa_end": null,
"aa_length": 1871,
"cds_start": 2247,
"cds_end": null,
"cds_length": 5616,
"cdna_start": 2464,
"cdna_end": null,
"cdna_length": 6044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATRX",
"gene_hgnc_id": 886,
"dbsnp": "rs1297294136",
"frequency_reference_population": 0.000021504522,
"hom_count_reference_population": 7,
"allele_count_reference_population": 26,
"gnomad_exomes_af": 0.000020042,
"gnomad_genomes_af": 0.0000359224,
"gnomad_exomes_ac": 22,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 3.405,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM4_Supporting,BP6,BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 5,
"pathogenic_score": 1,
"criteria": [
"PM4_Supporting",
"BP6",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000373344.11",
"gene_symbol": "ATRX",
"hgnc_id": 886,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "XL",
"hgvs_c": "c.2247_2249delTTC",
"hgvs_p": "p.Ser750del"
}
],
"clinvar_disease": "Alpha thalassemia-X-linked intellectual disability syndrome,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1",
"phenotype_combined": "Alpha thalassemia-X-linked intellectual disability syndrome|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}