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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-153932111-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153932111&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153932111,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000464845.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Trp",
"transcript": "NM_003491.4",
"protein_id": "NP_003482.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 235,
"cds_start": 346,
"cds_end": null,
"cds_length": 708,
"cdna_start": 479,
"cdna_end": null,
"cdna_length": 1603,
"mane_select": "ENST00000464845.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Trp",
"transcript": "ENST00000464845.6",
"protein_id": "ENSP00000417763.1",
"transcript_support_level": 1,
"aa_start": 116,
"aa_end": null,
"aa_length": 235,
"cds_start": 346,
"cds_end": null,
"cds_length": 708,
"cdna_start": 479,
"cdna_end": null,
"cdna_length": 1603,
"mane_select": "NM_003491.4",
"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": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "n.657C>T",
"hgvs_p": null,
"transcript": "ENST00000466877.5",
"protein_id": null,
"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": 1080,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.341+205C>T",
"hgvs_p": null,
"transcript": "ENST00000370009.5",
"protein_id": "ENSP00000359026.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 220,
"cds_start": -4,
"cds_end": null,
"cds_length": 663,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 837,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.328C>T",
"hgvs_p": "p.Arg110Trp",
"transcript": "NM_001256120.2",
"protein_id": "NP_001243049.1",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 229,
"cds_start": 328,
"cds_end": null,
"cds_length": 690,
"cdna_start": 461,
"cdna_end": null,
"cdna_length": 1585,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Trp",
"transcript": "ENST00000393712.7",
"protein_id": "ENSP00000377315.3",
"transcript_support_level": 5,
"aa_start": 116,
"aa_end": null,
"aa_length": 184,
"cds_start": 346,
"cds_end": null,
"cds_length": 555,
"cdna_start": 400,
"cdna_end": null,
"cdna_length": 908,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Trp",
"transcript": "ENST00000370015.8",
"protein_id": "ENSP00000359032.4",
"transcript_support_level": 5,
"aa_start": 116,
"aa_end": null,
"aa_length": 169,
"cds_start": 346,
"cds_end": null,
"cds_length": 510,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 1002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.328C>T",
"hgvs_p": "p.Arg110Trp",
"transcript": "ENST00000432089.1",
"protein_id": "ENSP00000413668.1",
"transcript_support_level": 3,
"aa_start": 110,
"aa_end": null,
"aa_length": 144,
"cds_start": 328,
"cds_end": null,
"cds_length": 437,
"cdna_start": 490,
"cdna_end": null,
"cdna_length": 599,
"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": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "n.457C>T",
"hgvs_p": null,
"transcript": "ENST00000393710.7",
"protein_id": null,
"transcript_support_level": 2,
"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": 525,
"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": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "n.635C>T",
"hgvs_p": null,
"transcript": "ENST00000460996.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 908,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "n.148C>T",
"hgvs_p": null,
"transcript": "ENST00000467451.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 743,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "n.722C>T",
"hgvs_p": null,
"transcript": "ENST00000477750.6",
"protein_id": null,
"transcript_support_level": 2,
"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": 2467,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "n.765C>T",
"hgvs_p": null,
"transcript": "ENST00000477882.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 809,
"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": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "n.565C>T",
"hgvs_p": null,
"transcript": "ENST00000484950.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 873,
"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": 6,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARHGAP4",
"gene_hgnc_id": 674,
"hgvs_c": "n.441C>T",
"hgvs_p": null,
"transcript": "ENST00000494813.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 1939,
"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": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "n.464C>T",
"hgvs_p": null,
"transcript": "ENST00000700299.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1954,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.341+205C>T",
"hgvs_p": null,
"transcript": "NM_001256119.2",
"protein_id": "NP_001243048.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 220,
"cds_start": -4,
"cds_end": null,
"cds_length": 663,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1558,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.323+205C>T",
"hgvs_p": null,
"transcript": "ENST00000370011.7",
"protein_id": "ENSP00000359028.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 141,
"cds_start": -4,
"cds_end": null,
"cds_length": 427,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 538,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"dbsnp": "rs587780563",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8318424224853516,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.435,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9744,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.11,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.303,
"phylop100way_prediction": "Uncertain_significance",
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PM5,PP2,PP3,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PM5",
"PP2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000464845.6",
"gene_symbol": "NAA10",
"hgnc_id": 18704,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,Unknown",
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Trp"
},
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000494813.5",
"gene_symbol": "ARHGAP4",
"hgnc_id": 674,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "n.441C>T",
"hgvs_p": null
}
],
"clinvar_disease": "NAA10-related disorder,Ogden syndrome,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:7 LP:1",
"phenotype_combined": "Ogden syndrome|not provided|NAA10-related disorder",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}