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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: 19-1912069-TGTCTCCCACAGTCG-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=1912069&ref=TGTCTCCCACAGTCG&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 1912069,
"ref": "TGTCTCCCACAGTCG",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "NM_138422.4",
"consequences": [
{
"aa_ref": "CLPQSA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ADAT3",
"gene_hgnc_id": 25151,
"hgvs_c": "c.24_37delTCTCCCACAGTCGG",
"hgvs_p": "p.Pro10fs",
"transcript": "NM_138422.4",
"protein_id": "NP_612431.2",
"transcript_support_level": null,
"aa_start": 8,
"aa_end": null,
"aa_length": 367,
"cds_start": 24,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 223,
"cdna_end": null,
"cdna_length": 1599,
"mane_select": "ENST00000329478.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "CLPQSA",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ADAT3",
"gene_hgnc_id": 25151,
"hgvs_c": "c.24_37delTCTCCCACAGTCGG",
"hgvs_p": "p.Pro10fs",
"transcript": "ENST00000329478.4",
"protein_id": "ENSP00000332448.2",
"transcript_support_level": 1,
"aa_start": 8,
"aa_end": null,
"aa_length": 367,
"cds_start": 24,
"cds_end": null,
"cds_length": 1104,
"cdna_start": 223,
"cdna_end": null,
"cdna_length": 1599,
"mane_select": "NM_138422.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCAMP4",
"gene_hgnc_id": 30385,
"hgvs_c": "c.-41-2908_-41-2895delTCTCCCACAGTCGG",
"hgvs_p": null,
"transcript": "NM_079834.4",
"protein_id": "NP_524558.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 229,
"cds_start": -4,
"cds_end": null,
"cds_length": 690,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2501,
"mane_select": "ENST00000316097.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCAMP4",
"gene_hgnc_id": 30385,
"hgvs_c": "c.-41-2908_-41-2895delTCTCCCACAGTCGG",
"hgvs_p": null,
"transcript": "ENST00000316097.13",
"protein_id": "ENSP00000316007.7",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 229,
"cds_start": -4,
"cds_end": null,
"cds_length": 690,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2501,
"mane_select": "NM_079834.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCAMP4",
"gene_hgnc_id": 30385,
"hgvs_c": "c.-125-5623_-125-5610delTCTCCCACAGTCGG",
"hgvs_p": null,
"transcript": "ENST00000414057.6",
"protein_id": "ENSP00000479672.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 139,
"cds_start": -4,
"cds_end": null,
"cds_length": 422,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1477,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "CLPQSA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ADAT3",
"gene_hgnc_id": 25151,
"hgvs_c": "c.24_37delTCTCCCACAGTCGG",
"hgvs_p": "p.Pro10fs",
"transcript": "ENST00000454697.1",
"protein_id": "ENSP00000404502.2",
"transcript_support_level": 3,
"aa_start": 8,
"aa_end": null,
"aa_length": 68,
"cds_start": 24,
"cds_end": null,
"cds_length": 208,
"cdna_start": 799,
"cdna_end": null,
"cdna_length": 983,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ADAT3",
"gene_hgnc_id": 25151,
"hgvs_c": "c.-15-10_-12delTCTCCCACAGTCGG",
"hgvs_p": null,
"transcript": "NM_001329533.2",
"protein_id": "NP_001316462.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 351,
"cds_start": -4,
"cds_end": null,
"cds_length": 1056,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"splice_region_variant",
"5_prime_UTR_variant",
"intron_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ADAT3",
"gene_hgnc_id": 25151,
"hgvs_c": "c.-15-10_-12delTCTCCCACAGTCGG",
"hgvs_p": null,
"transcript": "NM_001329533.2",
"protein_id": "NP_001316462.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 351,
"cds_start": -4,
"cds_end": null,
"cds_length": 1056,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCAMP4",
"gene_hgnc_id": 30385,
"hgvs_c": "c.-41-2908_-41-2895delTCTCCCACAGTCGG",
"hgvs_p": null,
"transcript": "NM_001329540.2",
"protein_id": "NP_001316469.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 195,
"cds_start": -4,
"cds_end": null,
"cds_length": 588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2399,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCAMP4",
"gene_hgnc_id": 30385,
"hgvs_c": "c.-41-2908_-41-2895delTCTCCCACAGTCGG",
"hgvs_p": null,
"transcript": "ENST00000409472.6",
"protein_id": "ENSP00000386865.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 195,
"cds_start": -4,
"cds_end": null,
"cds_length": 588,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2584,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCAMP4",
"gene_hgnc_id": 30385,
"hgvs_c": "c.-125-5623_-125-5610delTCTCCCACAGTCGG",
"hgvs_p": null,
"transcript": "NM_001329539.2",
"protein_id": "NP_001316468.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 185,
"cds_start": -4,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCAMP4",
"gene_hgnc_id": 30385,
"hgvs_c": "c.-41-2908_-41-2895delTCTCCCACAGTCGG",
"hgvs_p": null,
"transcript": "ENST00000411971.5",
"protein_id": "ENSP00000388185.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 122,
"cds_start": -4,
"cds_end": null,
"cds_length": 370,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCAMP4",
"gene_hgnc_id": 30385,
"hgvs_c": "c.-126+3436_-126+3449delTCTCCCACAGTCGG",
"hgvs_p": null,
"transcript": "ENST00000588907.2",
"protein_id": "ENSP00000478264.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 21,
"cds_start": -4,
"cds_end": null,
"cds_length": 67,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 547,
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCAMP4",
"gene_hgnc_id": 30385,
"hgvs_c": "n.69-2908_69-2895delTCTCCCACAGTCGG",
"hgvs_p": null,
"transcript": "ENST00000452128.6",
"protein_id": null,
"transcript_support_level": 2,
"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": 718,
"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": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCAMP4",
"gene_hgnc_id": 30385,
"hgvs_c": "n.-41-2908_-41-2895delTCTCCCACAGTCGG",
"hgvs_p": null,
"transcript": "ENST00000460767.5",
"protein_id": "ENSP00000481989.1",
"transcript_support_level": 4,
"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": 569,
"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": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SCAMP4",
"gene_hgnc_id": 30385,
"hgvs_c": "n.42-2908_42-2895delTCTCCCACAGTCGG",
"hgvs_p": null,
"transcript": "ENST00000489554.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"non_coding_transcript_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ADAT3",
"gene_hgnc_id": 25151,
"hgvs_c": "c.-15-10_-12delTCTCCCACAGTCGG",
"hgvs_p": null,
"transcript": "NM_001329533.2",
"protein_id": "NP_001316462.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 351,
"cds_start": -4,
"cds_end": null,
"cds_length": 1056,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ADAT3",
"gene_hgnc_id": 25151,
"dbsnp": "rs752360082",
"frequency_reference_population": 0.0001902746,
"hom_count_reference_population": 0,
"allele_count_reference_population": 274,
"gnomad_exomes_af": 0.000201897,
"gnomad_genomes_af": 0.0000919601,
"gnomad_exomes_ac": 260,
"gnomad_genomes_ac": 14,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 4.441,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_138422.4",
"gene_symbol": "ADAT3",
"hgnc_id": 25151,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.24_37delTCTCCCACAGTCGG",
"hgvs_p": "p.Pro10fs"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PP5_Very_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_079834.4",
"gene_symbol": "SCAMP4",
"hgnc_id": 30385,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-41-2908_-41-2895delTCTCCCACAGTCGG",
"hgvs_p": null
}
],
"clinvar_disease": "Intellectual disability-strabismus syndrome,not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:2",
"phenotype_combined": "not provided|Intellectual disability-strabismus syndrome",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}