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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-153930131-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153930131&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153930131,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_003491.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.564G>A",
"hgvs_p": "p.Pro188Pro",
"transcript": "NM_003491.4",
"protein_id": "NP_003482.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 235,
"cds_start": 564,
"cds_end": null,
"cds_length": 708,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000464845.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003491.4"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.564G>A",
"hgvs_p": "p.Pro188Pro",
"transcript": "ENST00000464845.6",
"protein_id": "ENSP00000417763.1",
"transcript_support_level": 1,
"aa_start": 188,
"aa_end": null,
"aa_length": 235,
"cds_start": 564,
"cds_end": null,
"cds_length": 708,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003491.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000464845.6"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.519G>A",
"hgvs_p": "p.Pro173Pro",
"transcript": "ENST00000370009.5",
"protein_id": "ENSP00000359026.1",
"transcript_support_level": 1,
"aa_start": 173,
"aa_end": null,
"aa_length": 220,
"cds_start": 519,
"cds_end": null,
"cds_length": 663,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370009.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "n.875G>A",
"hgvs_p": null,
"transcript": "ENST00000466877.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000466877.5"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.609G>A",
"hgvs_p": "p.Pro203Pro",
"transcript": "ENST00000930123.1",
"protein_id": "ENSP00000600182.1",
"transcript_support_level": null,
"aa_start": 203,
"aa_end": null,
"aa_length": 250,
"cds_start": 609,
"cds_end": null,
"cds_length": 753,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930123.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.546G>A",
"hgvs_p": "p.Pro182Pro",
"transcript": "NM_001256120.2",
"protein_id": "NP_001243049.1",
"transcript_support_level": null,
"aa_start": 182,
"aa_end": null,
"aa_length": 229,
"cds_start": 546,
"cds_end": null,
"cds_length": 690,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001256120.2"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.519G>A",
"hgvs_p": "p.Pro173Pro",
"transcript": "NM_001256119.2",
"protein_id": "NP_001243048.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 220,
"cds_start": 519,
"cds_end": null,
"cds_length": 663,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001256119.2"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.513G>A",
"hgvs_p": "p.Pro171Pro",
"transcript": "ENST00000930125.1",
"protein_id": "ENSP00000600184.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 218,
"cds_start": 513,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930125.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.465G>A",
"hgvs_p": "p.Pro155Pro",
"transcript": "ENST00000854040.1",
"protein_id": "ENSP00000524099.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 202,
"cds_start": 465,
"cds_end": null,
"cds_length": 609,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000854040.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.402G>A",
"hgvs_p": "p.Pro134Pro",
"transcript": "ENST00000930126.1",
"protein_id": "ENSP00000600185.1",
"transcript_support_level": null,
"aa_start": 134,
"aa_end": null,
"aa_length": 181,
"cds_start": 402,
"cds_end": null,
"cds_length": 546,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930126.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.384G>A",
"hgvs_p": "p.Pro128Pro",
"transcript": "ENST00000930124.1",
"protein_id": "ENSP00000600183.1",
"transcript_support_level": null,
"aa_start": 128,
"aa_end": null,
"aa_length": 175,
"cds_start": 384,
"cds_end": null,
"cds_length": 528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930124.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.*89G>A",
"hgvs_p": null,
"transcript": "ENST00000393712.7",
"protein_id": "ENSP00000377315.3",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 184,
"cds_start": null,
"cds_end": null,
"cds_length": 555,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000393712.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.*138G>A",
"hgvs_p": null,
"transcript": "ENST00000370015.8",
"protein_id": "ENSP00000359032.4",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 169,
"cds_start": null,
"cds_end": null,
"cds_length": 510,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370015.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "n.853G>A",
"hgvs_p": null,
"transcript": "ENST00000460996.5",
"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": "retained_intron",
"feature": "ENST00000460996.5"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "n.2163G>A",
"hgvs_p": null,
"transcript": "ENST00000477750.6",
"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": "retained_intron",
"feature": "ENST00000477750.6"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "n.783G>A",
"hgvs_p": null,
"transcript": "ENST00000484950.5",
"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": "retained_intron",
"feature": "ENST00000484950.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "n.1816G>A",
"hgvs_p": null,
"transcript": "ENST00000700299.1",
"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": "retained_intron",
"feature": "ENST00000700299.1"
},
{
"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": 14,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "ARHGAP4",
"gene_hgnc_id": 674,
"hgvs_c": "n.481+1940G>A",
"hgvs_p": null,
"transcript": "ENST00000494813.5",
"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": "ENST00000494813.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "c.*74G>A",
"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": null,
"cds_end": null,
"cds_length": 427,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370011.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"hgvs_c": "n.*162G>A",
"hgvs_p": null,
"transcript": "ENST00000467451.1",
"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": "retained_intron",
"feature": "ENST00000467451.1"
}
],
"gene_symbol": "NAA10",
"gene_hgnc_id": 18704,
"dbsnp": "rs150971216",
"frequency_reference_population": 0.00011828779,
"hom_count_reference_population": 58,
"allele_count_reference_population": 143,
"gnomad_exomes_af": 0.000123853,
"gnomad_genomes_af": 0.0000631552,
"gnomad_exomes_ac": 136,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7599999904632568,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.76,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.154,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_003491.4",
"gene_symbol": "NAA10",
"hgnc_id": 18704,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL,Unknown",
"hgvs_c": "c.564G>A",
"hgvs_p": "p.Pro188Pro"
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000494813.5",
"gene_symbol": "ARHGAP4",
"hgnc_id": 674,
"effects": [
"intron_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "n.481+1940G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 B:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}