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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: 9-83623182-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=83623182&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"gene_symbol": "IDNK",
"hgnc_id": 31367,
"hgvs_c": "c.-302C>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -2,
"transcript": "NM_001256915.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_score": -2,
"allele_count_reference_population": 15,
"alphamissense_prediction": null,
"alphamissense_score": 0.27,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.48,
"chr": "9",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.13600295782089233,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 187,
"aa_ref": "P",
"aa_start": 4,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 936,
"cdna_start": 40,
"cds_end": null,
"cds_length": 564,
"cds_start": 11,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001001551.4",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "c.11C>T",
"hgvs_p": "p.Pro4Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000376419.5",
"protein_coding": true,
"protein_id": "NP_001001551.2",
"strand": true,
"transcript": "NM_001001551.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 187,
"aa_ref": "P",
"aa_start": 4,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 936,
"cdna_start": 40,
"cds_end": null,
"cds_length": 564,
"cds_start": 11,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000376419.5",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "c.11C>T",
"hgvs_p": "p.Pro4Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001001551.4",
"protein_coding": true,
"protein_id": "ENSP00000365601.4",
"strand": true,
"transcript": "ENST00000376419.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1623,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000533522.1",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "n.11C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000434673.1",
"strand": true,
"transcript": "ENST00000533522.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 141,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1110,
"cdna_start": null,
"cds_end": null,
"cds_length": 426,
"cds_start": null,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001256915.2",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "c.-302C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001243844.1",
"strand": true,
"transcript": "NM_001256915.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 141,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1008,
"cdna_start": null,
"cds_end": null,
"cds_length": 426,
"cds_start": null,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001351535.2",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "c.-200C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001338464.1",
"strand": true,
"transcript": "NM_001351535.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 141,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1210,
"cdna_start": null,
"cds_end": null,
"cds_length": 426,
"cds_start": null,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000454393.5",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "c.-302C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000403290.2",
"strand": true,
"transcript": "ENST00000454393.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 89,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 607,
"cdna_start": null,
"cds_end": null,
"cds_length": 270,
"cds_start": null,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000530832.5",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "c.-302C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000436381.1",
"strand": true,
"transcript": "ENST00000530832.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 188,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5173,
"cdna_start": null,
"cds_end": null,
"cds_length": 567,
"cds_start": null,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_006717111.5",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "c.-4224C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006717174.1",
"strand": true,
"transcript": "XM_006717111.5",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 205,
"aa_ref": "P",
"aa_start": 4,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 986,
"cdna_start": 36,
"cds_end": null,
"cds_length": 618,
"cds_start": 11,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000904784.1",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "c.11C>T",
"hgvs_p": "p.Pro4Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574843.1",
"strand": true,
"transcript": "ENST00000904784.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 158,
"aa_ref": "P",
"aa_start": 4,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 951,
"cdna_start": 128,
"cds_end": null,
"cds_length": 477,
"cds_start": 11,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000904783.1",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "c.11C>T",
"hgvs_p": "p.Pro4Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574842.1",
"strand": true,
"transcript": "ENST00000904783.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 90,
"aa_ref": "P",
"aa_start": 4,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 511,
"cdna_start": 15,
"cds_end": null,
"cds_length": 273,
"cds_start": 11,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000376417.8",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "c.11C>T",
"hgvs_p": "p.Pro4Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000365599.4",
"strand": true,
"transcript": "ENST00000376417.8",
"transcript_support_level": 5
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 59,
"aa_ref": "P",
"aa_start": 4,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 629,
"cdna_start": 17,
"cds_end": null,
"cds_length": 180,
"cds_start": 11,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000405990.3",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "c.11C>T",
"hgvs_p": "p.Pro4Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000385324.2",
"strand": true,
"transcript": "ENST00000405990.3",
"transcript_support_level": 2
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 338,
"aa_ref": "A",
"aa_start": 54,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1375,
"cdna_start": 177,
"cds_end": null,
"cds_length": 1017,
"cds_start": 162,
"consequences": [
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_006717110.4",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "c.162C>T",
"hgvs_p": "p.Ala54Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006717173.2",
"strand": true,
"transcript": "XM_006717110.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 141,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1110,
"cdna_start": null,
"cds_end": null,
"cds_length": 426,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001256915.2",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "c.-302C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001243844.1",
"strand": true,
"transcript": "NM_001256915.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 141,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1008,
"cdna_start": null,
"cds_end": null,
"cds_length": 426,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001351535.2",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "c.-200C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001338464.1",
"strand": true,
"transcript": "NM_001351535.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 141,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1210,
"cdna_start": null,
"cds_end": null,
"cds_length": 426,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000454393.5",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "c.-302C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000403290.2",
"strand": true,
"transcript": "ENST00000454393.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 89,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 607,
"cdna_start": null,
"cds_end": null,
"cds_length": 270,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000530832.5",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "c.-302C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000436381.1",
"strand": true,
"transcript": "ENST00000530832.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 188,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5173,
"cdna_start": null,
"cds_end": null,
"cds_length": 567,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_006717111.5",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "c.-4224C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006717174.1",
"strand": true,
"transcript": "XM_006717111.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 905,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NR_046421.2",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "n.40C>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": "NR_046421.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1522,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NR_046422.2",
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"hgvs_c": "n.40C>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": "NR_046422.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs566045982",
"effect": "5_prime_UTR_premature_start_codon_gain_variant",
"frequency_reference_population": 0.000010611911,
"gene_hgnc_id": 31367,
"gene_symbol": "IDNK",
"gnomad_exomes_ac": 5,
"gnomad_exomes_af": 0.00000396359,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 10,
"gnomad_genomes_af": 0.00006578,
"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": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.277,
"pos": 83623182,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.067,
"splice_prediction_selected": "Benign",
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"splice_source_selected": "max_spliceai",
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"transcript": "NM_001256915.2"
}
]
}