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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: 5-178153709-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=178153709&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [],
"effects": [
"missense_variant"
],
"gene_symbol": "NHP2",
"hgnc_id": 14377,
"hgvs_c": "c.109C>T",
"hgvs_p": "p.Pro37Ser",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": 0,
"transcript": "NM_001396110.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_score": 0,
"allele_count_reference_population": 142,
"alphamissense_prediction": null,
"alphamissense_score": 0.9921,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.15,
"chr": "5",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Dyskeratosis congenita,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.7241395711898804,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 153,
"aa_ref": "P",
"aa_start": 37,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 780,
"cdna_start": 177,
"cds_end": null,
"cds_length": 462,
"cds_start": 109,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_017838.4",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.109C>T",
"hgvs_p": "p.Pro37Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000274606.8",
"protein_coding": true,
"protein_id": "NP_060308.1",
"strand": false,
"transcript": "NM_017838.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 153,
"aa_ref": "P",
"aa_start": 37,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 780,
"cdna_start": 177,
"cds_end": null,
"cds_length": 462,
"cds_start": 109,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000274606.8",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.109C>T",
"hgvs_p": "p.Pro37Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_017838.4",
"protein_coding": true,
"protein_id": "ENSP00000274606.4",
"strand": false,
"transcript": "ENST00000274606.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 566,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000510363.1",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "n.176C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000510363.1",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 168,
"aa_ref": "P",
"aa_start": 37,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 908,
"cdna_start": 177,
"cds_end": null,
"cds_length": 507,
"cds_start": 109,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001396110.1",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.109C>T",
"hgvs_p": "p.Pro37Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001383039.1",
"strand": false,
"transcript": "NM_001396110.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 159,
"aa_ref": "P",
"aa_start": 37,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 874,
"cdna_start": 253,
"cds_end": null,
"cds_length": 480,
"cds_start": 109,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000940843.1",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.109C>T",
"hgvs_p": "p.Pro37Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610902.1",
"strand": false,
"transcript": "ENST00000940843.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 134,
"aa_ref": "P",
"aa_start": 37,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 472,
"cdna_start": 174,
"cds_end": null,
"cds_length": 407,
"cds_start": 109,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000514354.5",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.109C>T",
"hgvs_p": "p.Pro37Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000423803.1",
"strand": false,
"transcript": "ENST00000514354.5",
"transcript_support_level": 3
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 131,
"aa_ref": "P",
"aa_start": 37,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 475,
"cdna_start": 186,
"cds_end": null,
"cds_length": 398,
"cds_start": 109,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000511078.1",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.109C>T",
"hgvs_p": "p.Pro37Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000423849.1",
"strand": false,
"transcript": "ENST00000511078.1",
"transcript_support_level": 2
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 130,
"aa_ref": "P",
"aa_start": 37,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 710,
"cdna_start": 176,
"cds_end": null,
"cds_length": 393,
"cds_start": 109,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000890268.1",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.109C>T",
"hgvs_p": "p.Pro37Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000560327.1",
"strand": false,
"transcript": "ENST00000890268.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 114,
"aa_ref": "P",
"aa_start": 37,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 697,
"cdna_start": 207,
"cds_end": null,
"cds_length": 345,
"cds_start": 109,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000940844.1",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.109C>T",
"hgvs_p": "p.Pro37Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610903.1",
"strand": false,
"transcript": "ENST00000940844.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 90,
"aa_ref": "P",
"aa_start": 37,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 674,
"cdna_start": 177,
"cds_end": null,
"cds_length": 273,
"cds_start": 109,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001034833.2",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.109C>T",
"hgvs_p": "p.Pro37Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001030005.1",
"strand": false,
"transcript": "NM_001034833.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 90,
"aa_ref": "P",
"aa_start": 37,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 637,
"cdna_start": 140,
"cds_end": null,
"cds_length": 273,
"cds_start": 109,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000314397.9",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.109C>T",
"hgvs_p": "p.Pro37Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000366276.2",
"strand": false,
"transcript": "ENST00000314397.9",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 552,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000502263.1",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "n.-130C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000502263.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 613,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000697323.1",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "n.-88C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000697323.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs201390429",
"effect": "missense_variant",
"frequency_reference_population": 0.00008798497,
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"gnomad_exomes_ac": 138,
"gnomad_exomes_af": 0.000094412,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.0000262753,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Dyskeratosis congenita|not specified|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.446,
"pos": 178153709,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.396,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001396110.1"
}
]
}