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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: 15-64156802-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=64156802&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 64156802,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000300026.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIB",
"gene_hgnc_id": 9255,
"hgvs_c": "c.451C>T",
"hgvs_p": "p.Gln151*",
"transcript": "NM_000942.5",
"protein_id": "NP_000933.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 216,
"cds_start": 451,
"cds_end": null,
"cds_length": 651,
"cdna_start": 487,
"cdna_end": null,
"cdna_length": 893,
"mane_select": "ENST00000300026.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIB",
"gene_hgnc_id": 9255,
"hgvs_c": "c.451C>T",
"hgvs_p": "p.Gln151*",
"transcript": "ENST00000300026.4",
"protein_id": "ENSP00000300026.4",
"transcript_support_level": 1,
"aa_start": 151,
"aa_end": null,
"aa_length": 216,
"cds_start": 451,
"cds_end": null,
"cds_length": 651,
"cdna_start": 487,
"cdna_end": null,
"cdna_length": 893,
"mane_select": "NM_000942.5",
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX22",
"gene_hgnc_id": 16315,
"hgvs_c": "n.2689G>A",
"hgvs_p": null,
"transcript": "ENST00000560997.1",
"protein_id": null,
"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": 3367,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIB",
"gene_hgnc_id": 9255,
"hgvs_c": "n.3678C>T",
"hgvs_p": null,
"transcript": "ENST00000561048.2",
"protein_id": null,
"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": 4064,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX22",
"gene_hgnc_id": 16315,
"hgvs_c": "c.*2294G>A",
"hgvs_p": null,
"transcript": "NM_024798.3",
"protein_id": "NP_079074.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 193,
"cds_start": -4,
"cds_end": null,
"cds_length": 582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3600,
"mane_select": "ENST00000325881.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX22",
"gene_hgnc_id": 16315,
"hgvs_c": "c.*2294G>A",
"hgvs_p": null,
"transcript": "ENST00000325881.9",
"protein_id": "ENSP00000323435.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 193,
"cds_start": -4,
"cds_end": null,
"cds_length": 582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3600,
"mane_select": "NM_024798.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIB",
"gene_hgnc_id": 9255,
"hgvs_c": "c.451C>T",
"hgvs_p": "p.Gln151*",
"transcript": "ENST00000681397.1",
"protein_id": "ENSP00000506584.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 216,
"cds_start": 451,
"cds_end": null,
"cds_length": 651,
"cdna_start": 490,
"cdna_end": null,
"cdna_length": 973,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIB",
"gene_hgnc_id": 9255,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Gln116*",
"transcript": "ENST00000681658.1",
"protein_id": "ENSP00000505431.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 181,
"cds_start": 346,
"cds_end": null,
"cds_length": 546,
"cdna_start": 386,
"cdna_end": null,
"cdna_length": 869,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIB",
"gene_hgnc_id": 9255,
"hgvs_c": "c.277C>T",
"hgvs_p": "p.Gln93*",
"transcript": "ENST00000718123.1",
"protein_id": "ENSP00000520679.1",
"transcript_support_level": null,
"aa_start": 93,
"aa_end": null,
"aa_length": 158,
"cds_start": 277,
"cds_end": null,
"cds_length": 477,
"cdna_start": 303,
"cdna_end": null,
"cdna_length": 694,
"mane_select": null,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX22",
"gene_hgnc_id": 16315,
"hgvs_c": "n.3034G>A",
"hgvs_p": null,
"transcript": "ENST00000557789.5",
"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": 3713,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIB",
"gene_hgnc_id": 9255,
"hgvs_c": "n.357C>T",
"hgvs_p": null,
"transcript": "ENST00000558492.1",
"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": 381,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIB",
"gene_hgnc_id": 9255,
"hgvs_c": "n.*124C>T",
"hgvs_p": null,
"transcript": "ENST00000680158.1",
"protein_id": "ENSP00000504873.1",
"transcript_support_level": null,
"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": 1050,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIB",
"gene_hgnc_id": 9255,
"hgvs_c": "n.405C>T",
"hgvs_p": null,
"transcript": "ENST00000680343.1",
"protein_id": null,
"transcript_support_level": null,
"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": 888,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIB",
"gene_hgnc_id": 9255,
"hgvs_c": "n.*279C>T",
"hgvs_p": null,
"transcript": "ENST00000718122.1",
"protein_id": "ENSP00000520678.1",
"transcript_support_level": null,
"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": 927,
"mane_select": null,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX22",
"gene_hgnc_id": 16315,
"hgvs_c": "n.2968G>A",
"hgvs_p": null,
"transcript": "NR_073534.2",
"protein_id": null,
"transcript_support_level": null,
"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": 3647,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIB",
"gene_hgnc_id": 9255,
"hgvs_c": "n.*124C>T",
"hgvs_p": null,
"transcript": "ENST00000680158.1",
"protein_id": "ENSP00000504873.1",
"transcript_support_level": null,
"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": 1050,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPIB",
"gene_hgnc_id": 9255,
"hgvs_c": "n.*279C>T",
"hgvs_p": null,
"transcript": "ENST00000718122.1",
"protein_id": "ENSP00000520678.1",
"transcript_support_level": null,
"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": 927,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX22",
"gene_hgnc_id": 16315,
"hgvs_c": "c.*2294G>A",
"hgvs_p": null,
"transcript": "XM_017022581.2",
"protein_id": "XP_016878070.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 165,
"cds_start": -4,
"cds_end": null,
"cds_length": 498,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3516,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PPIB",
"gene_hgnc_id": 9255,
"dbsnp": "rs121434559",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5899999737739563,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.10000000149011612,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.59,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.457,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.1,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000300026.4",
"gene_symbol": "PPIB",
"hgnc_id": 9255,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.451C>T",
"hgvs_p": "p.Gln151*"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000325881.9",
"gene_symbol": "SNX22",
"hgnc_id": 16315,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*2294G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Osteogenesis imperfecta type 9,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1 O:1",
"phenotype_combined": "Osteogenesis imperfecta type 9|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}