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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-70035434-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=70035434&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"PM1",
"PP2",
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "EDA",
"hgnc_id": 3157,
"hgvs_c": "c.1001G>A",
"hgvs_p": "p.Arg334His",
"inheritance_mode": "XL,AD",
"pathogenic_score": 3,
"score": -17,
"transcript": "NM_001399.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "PM1,PP2,BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_score": -17,
"allele_count_reference_population": 461,
"alphamissense_prediction": null,
"alphamissense_score": 0.8704,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.34,
"chr": "X",
"clinvar_classification": "Benign",
"clinvar_disease": " 1, X-linked, selective,Hypohidrotic X-linked ectodermal dysplasia,See cases,Tooth agenesis,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.010842382907867432,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 391,
"aa_ref": "R",
"aa_start": 334,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5235,
"cdna_start": 1197,
"cds_end": null,
"cds_length": 1176,
"cds_start": 1001,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001399.5",
"gene_hgnc_id": 3157,
"gene_symbol": "EDA",
"hgvs_c": "c.1001G>A",
"hgvs_p": "p.Arg334His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000374552.9",
"protein_coding": true,
"protein_id": "NP_001390.1",
"strand": true,
"transcript": "NM_001399.5",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 391,
"aa_ref": "R",
"aa_start": 334,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5235,
"cdna_start": 1197,
"cds_end": null,
"cds_length": 1176,
"cds_start": 1001,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000374552.9",
"gene_hgnc_id": 3157,
"gene_symbol": "EDA",
"hgvs_c": "c.1001G>A",
"hgvs_p": "p.Arg334His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001399.5",
"protein_coding": true,
"protein_id": "ENSP00000363680.4",
"strand": true,
"transcript": "ENST00000374552.9",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 389,
"aa_ref": "R",
"aa_start": 332,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5272,
"cdna_start": 1237,
"cds_end": null,
"cds_length": 1170,
"cds_start": 995,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000374553.6",
"gene_hgnc_id": 3157,
"gene_symbol": "EDA",
"hgvs_c": "c.995G>A",
"hgvs_p": "p.Arg332His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000363681.2",
"strand": true,
"transcript": "ENST00000374553.6",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 386,
"aa_ref": "R",
"aa_start": 329,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1381,
"cdna_start": 1178,
"cds_end": null,
"cds_length": 1161,
"cds_start": 986,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000524573.5",
"gene_hgnc_id": 3157,
"gene_symbol": "EDA",
"hgvs_c": "c.986G>A",
"hgvs_p": "p.Arg329His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000432585.1",
"strand": true,
"transcript": "ENST00000524573.5",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 389,
"aa_ref": "R",
"aa_start": 332,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5229,
"cdna_start": 1191,
"cds_end": null,
"cds_length": 1170,
"cds_start": 995,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001005609.2",
"gene_hgnc_id": 3157,
"gene_symbol": "EDA",
"hgvs_c": "c.995G>A",
"hgvs_p": "p.Arg332His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001005609.1",
"strand": true,
"transcript": "NM_001005609.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 388,
"aa_ref": "R",
"aa_start": 331,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5226,
"cdna_start": 1188,
"cds_end": null,
"cds_length": 1167,
"cds_start": 992,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001440761.1",
"gene_hgnc_id": 3157,
"gene_symbol": "EDA",
"hgvs_c": "c.992G>A",
"hgvs_p": "p.Arg331His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001427690.1",
"strand": true,
"transcript": "NM_001440761.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 386,
"aa_ref": "R",
"aa_start": 329,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5220,
"cdna_start": 1182,
"cds_end": null,
"cds_length": 1161,
"cds_start": 986,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001005612.3",
"gene_hgnc_id": 3157,
"gene_symbol": "EDA",
"hgvs_c": "c.986G>A",
"hgvs_p": "p.Arg329His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001005612.2",
"strand": true,
"transcript": "NM_001005612.3",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 377,
"aa_ref": "R",
"aa_start": 320,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5193,
"cdna_start": 1155,
"cds_end": null,
"cds_length": 1134,
"cds_start": 959,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001440762.1",
"gene_hgnc_id": 3157,
"gene_symbol": "EDA",
"hgvs_c": "c.959G>A",
"hgvs_p": "p.Arg320His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001427691.1",
"strand": true,
"transcript": "NM_001440762.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 259,
"aa_ref": "R",
"aa_start": 202,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4643,
"cdna_start": 608,
"cds_end": null,
"cds_length": 780,
"cds_start": 605,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000616899.1",
"gene_hgnc_id": 3157,
"gene_symbol": "EDA",
"hgvs_c": "c.605G>A",
"hgvs_p": "p.Arg202His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000481963.1",
"strand": true,
"transcript": "ENST00000616899.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs142948132",
"effect": "missense_variant",
"frequency_reference_population": 0.00038171635,
"gene_hgnc_id": 3157,
"gene_symbol": "EDA",
"gnomad_exomes_ac": 389,
"gnomad_exomes_af": 0.000354419,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_ac": 72,
"gnomad_genomes_af": 0.000653767,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 141,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "Tooth agenesis, selective, X-linked, 1|See cases|not provided|Hypohidrotic X-linked ectodermal dysplasia|Hypohidrotic X-linked ectodermal dysplasia;Tooth agenesis, selective, X-linked, 1",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.248,
"pos": 70035434,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.769,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_001399.5"
}
]
}