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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: 9-97675507-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=97675507&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 97675507,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000380.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "c.754C>G",
"hgvs_p": "p.Leu252Val",
"transcript": "NM_000380.4",
"protein_id": "NP_000371.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 273,
"cds_start": 754,
"cds_end": null,
"cds_length": 822,
"cdna_start": 802,
"cdna_end": null,
"cdna_length": 1400,
"mane_select": "ENST00000375128.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000380.4"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "c.754C>G",
"hgvs_p": "p.Leu252Val",
"transcript": "ENST00000375128.5",
"protein_id": "ENSP00000364270.5",
"transcript_support_level": 1,
"aa_start": 252,
"aa_end": null,
"aa_length": 273,
"cds_start": 754,
"cds_end": null,
"cds_length": 822,
"cdna_start": 802,
"cdna_end": null,
"cdna_length": 1400,
"mane_select": "NM_000380.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375128.5"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "c.628C>G",
"hgvs_p": "p.Leu210Val",
"transcript": "NM_001354975.2",
"protein_id": "NP_001341904.1",
"transcript_support_level": null,
"aa_start": 210,
"aa_end": null,
"aa_length": 231,
"cds_start": 628,
"cds_end": null,
"cds_length": 696,
"cdna_start": 1825,
"cdna_end": null,
"cdna_length": 2423,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001354975.2"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "c.487C>G",
"hgvs_p": "p.Leu163Val",
"transcript": "ENST00000905837.1",
"protein_id": "ENSP00000575896.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 184,
"cds_start": 487,
"cds_end": null,
"cds_length": 555,
"cdna_start": 528,
"cdna_end": null,
"cdna_length": 666,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905837.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "c.364C>G",
"hgvs_p": "p.Leu122Val",
"transcript": "ENST00000905836.1",
"protein_id": "ENSP00000575895.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 143,
"cds_start": 364,
"cds_end": null,
"cds_length": 432,
"cdna_start": 405,
"cdna_end": null,
"cdna_length": 1002,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905836.1"
},
{
"aa_ref": "L",
"aa_alt": "V",
"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": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "c.754C>G",
"hgvs_p": "p.Leu252Val",
"transcript": "XM_006717278.2",
"protein_id": "XP_006717341.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 262,
"cds_start": 754,
"cds_end": null,
"cds_length": 789,
"cdna_start": 802,
"cdna_end": null,
"cdna_length": 1147,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006717278.2"
},
{
"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": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "n.*190C>G",
"hgvs_p": null,
"transcript": "ENST00000462523.5",
"protein_id": "ENSP00000433006.1",
"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": 1584,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000462523.5"
},
{
"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": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "n.266C>G",
"hgvs_p": null,
"transcript": "ENST00000485042.1",
"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": 706,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000485042.1"
},
{
"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": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "n.1033C>G",
"hgvs_p": null,
"transcript": "NR_027302.2",
"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": 1631,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_027302.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "n.530C>G",
"hgvs_p": null,
"transcript": "NR_149091.2",
"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": 1128,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_149091.2"
},
{
"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": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "n.696C>G",
"hgvs_p": null,
"transcript": "NR_149092.2",
"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": 1294,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_149092.2"
},
{
"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": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "n.1222C>G",
"hgvs_p": null,
"transcript": "NR_149093.2",
"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": 1820,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_149093.2"
},
{
"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": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "n.1116C>G",
"hgvs_p": null,
"transcript": "NR_149094.2",
"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": 1714,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_149094.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"hgvs_c": "n.*190C>G",
"hgvs_p": null,
"transcript": "ENST00000462523.5",
"protein_id": "ENSP00000433006.1",
"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": 1584,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000462523.5"
}
],
"gene_symbol": "XPA",
"gene_hgnc_id": 12814,
"dbsnp": "rs3176750",
"frequency_reference_population": 0.0018322826,
"hom_count_reference_population": 37,
"allele_count_reference_population": 2957,
"gnomad_exomes_af": 0.000997435,
"gnomad_genomes_af": 0.0098564,
"gnomad_exomes_ac": 1458,
"gnomad_genomes_ac": 1499,
"gnomad_exomes_homalt": 12,
"gnomad_genomes_homalt": 25,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.001720130443572998,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.034,
"revel_prediction": "Benign",
"alphamissense_score": 0.0647,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.056,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_000380.4",
"gene_symbol": "XPA",
"hgnc_id": 12814,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.754C>G",
"hgvs_p": "p.Leu252Val"
}
],
"clinvar_disease": "Xeroderma pigmentosum group A,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:1 O:1",
"phenotype_combined": "not specified|Xeroderma pigmentosum group A|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}