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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: 12-68735334-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=68735334&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 68735334,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000229179.9",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP107",
"gene_hgnc_id": 29914,
"hgvs_c": "c.2492A>C",
"hgvs_p": "p.Asp831Ala",
"transcript": "NM_020401.4",
"protein_id": "NP_065134.1",
"transcript_support_level": null,
"aa_start": 831,
"aa_end": null,
"aa_length": 925,
"cds_start": 2492,
"cds_end": null,
"cds_length": 2778,
"cdna_start": 2580,
"cdna_end": null,
"cdna_length": 6213,
"mane_select": "ENST00000229179.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP107",
"gene_hgnc_id": 29914,
"hgvs_c": "c.2492A>C",
"hgvs_p": "p.Asp831Ala",
"transcript": "ENST00000229179.9",
"protein_id": "ENSP00000229179.4",
"transcript_support_level": 1,
"aa_start": 831,
"aa_end": null,
"aa_length": 925,
"cds_start": 2492,
"cds_end": null,
"cds_length": 2778,
"cdna_start": 2580,
"cdna_end": null,
"cdna_length": 6213,
"mane_select": "NM_020401.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP107",
"gene_hgnc_id": 29914,
"hgvs_c": "n.*1771A>C",
"hgvs_p": null,
"transcript": "ENST00000535718.5",
"protein_id": "ENSP00000445567.1",
"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": 2655,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP107",
"gene_hgnc_id": 29914,
"hgvs_c": "n.*1771A>C",
"hgvs_p": null,
"transcript": "ENST00000535718.5",
"protein_id": "ENSP00000445567.1",
"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": 2655,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP107",
"gene_hgnc_id": 29914,
"hgvs_c": "c.2405A>C",
"hgvs_p": "p.Asp802Ala",
"transcript": "NM_001330192.2",
"protein_id": "NP_001317121.1",
"transcript_support_level": null,
"aa_start": 802,
"aa_end": null,
"aa_length": 896,
"cds_start": 2405,
"cds_end": null,
"cds_length": 2691,
"cdna_start": 2608,
"cdna_end": null,
"cdna_length": 6241,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP107",
"gene_hgnc_id": 29914,
"hgvs_c": "c.2405A>C",
"hgvs_p": "p.Asp802Ala",
"transcript": "ENST00000539906.5",
"protein_id": "ENSP00000441448.1",
"transcript_support_level": 2,
"aa_start": 802,
"aa_end": null,
"aa_length": 896,
"cds_start": 2405,
"cds_end": null,
"cds_length": 2691,
"cdna_start": 2649,
"cdna_end": null,
"cdna_length": 3004,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP107",
"gene_hgnc_id": 29914,
"hgvs_c": "c.1775A>C",
"hgvs_p": "p.Asp592Ala",
"transcript": "ENST00000378905.6",
"protein_id": "ENSP00000368185.2",
"transcript_support_level": 5,
"aa_start": 592,
"aa_end": null,
"aa_length": 686,
"cds_start": 1775,
"cds_end": null,
"cds_length": 2061,
"cdna_start": 2343,
"cdna_end": null,
"cdna_length": 2859,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP107",
"gene_hgnc_id": 29914,
"hgvs_c": "c.2432A>C",
"hgvs_p": "p.Asp811Ala",
"transcript": "XM_005269037.5",
"protein_id": "XP_005269094.1",
"transcript_support_level": null,
"aa_start": 811,
"aa_end": null,
"aa_length": 905,
"cds_start": 2432,
"cds_end": null,
"cds_length": 2718,
"cdna_start": 2520,
"cdna_end": null,
"cdna_length": 6153,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUP107",
"gene_hgnc_id": 29914,
"hgvs_c": "c.1556A>C",
"hgvs_p": "p.Asp519Ala",
"transcript": "XM_047429177.1",
"protein_id": "XP_047285133.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 613,
"cds_start": 1556,
"cds_end": null,
"cds_length": 1842,
"cdna_start": 2738,
"cdna_end": null,
"cdna_length": 6371,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NUP107",
"gene_hgnc_id": 29914,
"hgvs_c": "n.234+2528A>C",
"hgvs_p": null,
"transcript": "ENST00000401003.3",
"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": 729,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NUP107",
"gene_hgnc_id": 29914,
"dbsnp": "rs864321632",
"frequency_reference_population": 0.00000616202,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000616202,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.96470707654953,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.528,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8194,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.46,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.261,
"phylop100way_prediction": "Pathogenic",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000229179.9",
"gene_symbol": "NUP107",
"hgnc_id": 29914,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2492A>C",
"hgvs_p": "p.Asp831Ala"
}
],
"clinvar_disease": " type 11,Nephrotic syndrome",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Nephrotic syndrome, type 11",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}