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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-70454271-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=70454271&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 70454271,
"ref": "C",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_021120.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.1360C>A",
"hgvs_p": "p.Arg454Arg",
"transcript": "NM_021120.4",
"protein_id": "NP_066943.2",
"transcript_support_level": null,
"aa_start": 454,
"aa_end": null,
"aa_length": 817,
"cds_start": 1360,
"cds_end": null,
"cds_length": 2454,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000374360.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_021120.4"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.1360C>A",
"hgvs_p": "p.Arg454Arg",
"transcript": "ENST00000374360.8",
"protein_id": "ENSP00000363480.3",
"transcript_support_level": 1,
"aa_start": 454,
"aa_end": null,
"aa_length": 817,
"cds_start": 1360,
"cds_end": null,
"cds_length": 2454,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_021120.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000374360.8"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.349C>A",
"hgvs_p": "p.Arg117Arg",
"transcript": "ENST00000374355.8",
"protein_id": "ENSP00000363475.3",
"transcript_support_level": 1,
"aa_start": 117,
"aa_end": null,
"aa_length": 512,
"cds_start": 349,
"cds_end": null,
"cds_length": 1539,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000374355.8"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.1414C>A",
"hgvs_p": "p.Arg472Arg",
"transcript": "ENST00000194900.8",
"protein_id": "ENSP00000194900.4",
"transcript_support_level": 5,
"aa_start": 472,
"aa_end": null,
"aa_length": 849,
"cds_start": 1414,
"cds_end": null,
"cds_length": 2550,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000194900.8"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.1360C>A",
"hgvs_p": "p.Arg454Arg",
"transcript": "ENST00000949779.1",
"protein_id": "ENSP00000619838.1",
"transcript_support_level": null,
"aa_start": 454,
"aa_end": null,
"aa_length": 831,
"cds_start": 1360,
"cds_end": null,
"cds_length": 2496,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949779.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.349C>A",
"hgvs_p": "p.Arg117Arg",
"transcript": "NM_020730.3",
"protein_id": "NP_065781.1",
"transcript_support_level": null,
"aa_start": 117,
"aa_end": null,
"aa_length": 512,
"cds_start": 349,
"cds_end": null,
"cds_length": 1539,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020730.3"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.1360C>A",
"hgvs_p": "p.Arg454Arg",
"transcript": "XM_006724625.3",
"protein_id": "XP_006724688.1",
"transcript_support_level": null,
"aa_start": 454,
"aa_end": null,
"aa_length": 849,
"cds_start": 1360,
"cds_end": null,
"cds_length": 2550,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006724625.3"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.1360C>A",
"hgvs_p": "p.Arg454Arg",
"transcript": "XM_011530883.2",
"protein_id": "XP_011529185.1",
"transcript_support_level": null,
"aa_start": 454,
"aa_end": null,
"aa_length": 835,
"cds_start": 1360,
"cds_end": null,
"cds_length": 2508,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011530883.2"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.1360C>A",
"hgvs_p": "p.Arg454Arg",
"transcript": "XM_006724626.3",
"protein_id": "XP_006724689.1",
"transcript_support_level": null,
"aa_start": 454,
"aa_end": null,
"aa_length": 831,
"cds_start": 1360,
"cds_end": null,
"cds_length": 2496,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006724626.3"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.349C>A",
"hgvs_p": "p.Arg117Arg",
"transcript": "XM_017029322.3",
"protein_id": "XP_016884811.1",
"transcript_support_level": null,
"aa_start": 117,
"aa_end": null,
"aa_length": 498,
"cds_start": 349,
"cds_end": null,
"cds_length": 1497,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029322.3"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.349C>A",
"hgvs_p": "p.Arg117Arg",
"transcript": "XM_017029323.3",
"protein_id": "XP_016884812.1",
"transcript_support_level": null,
"aa_start": 117,
"aa_end": null,
"aa_length": 494,
"cds_start": 349,
"cds_end": null,
"cds_length": 1485,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029323.3"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.349C>A",
"hgvs_p": "p.Arg117Arg",
"transcript": "XM_017029324.3",
"protein_id": "XP_016884813.1",
"transcript_support_level": null,
"aa_start": 117,
"aa_end": null,
"aa_length": 480,
"cds_start": 349,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029324.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "c.-90C>A",
"hgvs_p": null,
"transcript": "XM_005262248.5",
"protein_id": "XP_005262305.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 366,
"cds_start": null,
"cds_end": null,
"cds_length": 1101,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005262248.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"hgvs_c": "n.1759C>A",
"hgvs_p": null,
"transcript": "ENST00000463252.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000463252.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DLG3-AS1",
"gene_hgnc_id": 40182,
"hgvs_c": "n.84-965G>T",
"hgvs_p": null,
"transcript": "ENST00000424211.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000424211.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DLG3-AS1",
"gene_hgnc_id": 40182,
"hgvs_c": "n.134-965G>T",
"hgvs_p": null,
"transcript": "ENST00000431103.2",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000431103.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DLG3-AS1",
"gene_hgnc_id": 40182,
"hgvs_c": "n.84-965G>T",
"hgvs_p": null,
"transcript": "NR_046586.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_046586.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DLG3-AS1",
"gene_hgnc_id": 40182,
"hgvs_c": "n.51-965G>T",
"hgvs_p": null,
"transcript": "NR_109801.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_109801.1"
}
],
"gene_symbol": "DLG3",
"gene_hgnc_id": 2902,
"dbsnp": "rs769457554",
"frequency_reference_population": 0.000005465208,
"hom_count_reference_population": 2,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000546521,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.12999999523162842,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"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": -0.13,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.375,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BP7,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP7",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_021120.4",
"gene_symbol": "DLG3",
"hgnc_id": 2902,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1360C>A",
"hgvs_p": "p.Arg454Arg"
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000424211.1",
"gene_symbol": "DLG3-AS1",
"hgnc_id": 40182,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.84-965G>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}