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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: 1-225921254-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=225921254&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PM5",
"PP2",
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PYCR2",
"hgnc_id": 30262,
"hgvs_c": "c.751C>A",
"hgvs_p": "p.Arg251Ser",
"inheritance_mode": "AR",
"pathogenic_score": 7,
"score": 7,
"transcript": "NM_013328.4",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PM5",
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ENSG00000255835",
"hgnc_id": null,
"hgvs_c": "c.529C>A",
"hgvs_p": "p.Arg177Ser",
"inheritance_mode": "",
"pathogenic_score": 6,
"score": 6,
"transcript": "ENST00000432920.2",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP2,PP3_Moderate",
"acmg_score": 7,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.9556,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.21,
"chr": "1",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9361163973808289,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 320,
"aa_ref": "R",
"aa_start": 251,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1680,
"cdna_start": 891,
"cds_end": null,
"cds_length": 963,
"cds_start": 751,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_013328.4",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.751C>A",
"hgvs_p": "p.Arg251Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000343818.11",
"protein_coding": true,
"protein_id": "NP_037460.2",
"strand": false,
"transcript": "NM_013328.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 320,
"aa_ref": "R",
"aa_start": 251,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1680,
"cdna_start": 891,
"cds_end": null,
"cds_length": 963,
"cds_start": 751,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000343818.11",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.751C>A",
"hgvs_p": "p.Arg251Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_013328.4",
"protein_coding": true,
"protein_id": "ENSP00000342502.6",
"strand": false,
"transcript": "ENST00000343818.11",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 359,
"aa_ref": "R",
"aa_start": 177,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1625,
"cdna_start": 697,
"cds_end": null,
"cds_length": 1080,
"cds_start": 529,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000432920.2",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000255835",
"hgvs_c": "c.529C>A",
"hgvs_p": "p.Arg177Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000414068.2",
"strand": false,
"transcript": "ENST00000432920.2",
"transcript_support_level": 2
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 319,
"aa_ref": "R",
"aa_start": 250,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2232,
"cdna_start": 962,
"cds_end": null,
"cds_length": 960,
"cds_start": 748,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000872062.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.748C>A",
"hgvs_p": "p.Arg250Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542121.1",
"strand": false,
"transcript": "ENST00000872062.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 319,
"aa_ref": "R",
"aa_start": 250,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1740,
"cdna_start": 951,
"cds_end": null,
"cds_length": 960,
"cds_start": 748,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000872065.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.748C>A",
"hgvs_p": "p.Arg250Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542124.1",
"strand": false,
"transcript": "ENST00000872065.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 318,
"aa_ref": "R",
"aa_start": 249,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1688,
"cdna_start": 906,
"cds_end": null,
"cds_length": 957,
"cds_start": 745,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000931949.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.745C>A",
"hgvs_p": "p.Arg249Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000602007.1",
"strand": false,
"transcript": "ENST00000931949.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 297,
"aa_ref": "R",
"aa_start": 228,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1630,
"cdna_start": 842,
"cds_end": null,
"cds_length": 894,
"cds_start": 682,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000931947.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.682C>A",
"hgvs_p": "p.Arg228Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000602005.1",
"strand": false,
"transcript": "ENST00000931947.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 295,
"aa_ref": "R",
"aa_start": 226,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1603,
"cdna_start": 816,
"cds_end": null,
"cds_length": 888,
"cds_start": 676,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000872071.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.676C>A",
"hgvs_p": "p.Arg226Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542130.1",
"strand": false,
"transcript": "ENST00000872071.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 289,
"aa_ref": "R",
"aa_start": 220,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1661,
"cdna_start": 872,
"cds_end": null,
"cds_length": 870,
"cds_start": 658,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000872063.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.658C>A",
"hgvs_p": "p.Arg220Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542122.1",
"strand": false,
"transcript": "ENST00000872063.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 288,
"aa_ref": "R",
"aa_start": 219,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1617,
"cdna_start": 827,
"cds_end": null,
"cds_length": 867,
"cds_start": 655,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000954487.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.655C>A",
"hgvs_p": "p.Arg219Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000624546.1",
"strand": false,
"transcript": "ENST00000954487.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 288,
"aa_ref": "R",
"aa_start": 219,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1480,
"cdna_start": 692,
"cds_end": null,
"cds_length": 867,
"cds_start": 655,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000954488.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.655C>A",
"hgvs_p": "p.Arg219Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000624547.1",
"strand": false,
"transcript": "ENST00000954488.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 260,
"aa_ref": "R",
"aa_start": 191,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1523,
"cdna_start": 738,
"cds_end": null,
"cds_length": 783,
"cds_start": 571,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000872068.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.571C>A",
"hgvs_p": "p.Arg191Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542128.1",
"strand": false,
"transcript": "ENST00000872068.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 246,
"aa_ref": "R",
"aa_start": 177,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1458,
"cdna_start": 669,
"cds_end": null,
"cds_length": 741,
"cds_start": 529,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001271681.2",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.529C>A",
"hgvs_p": "p.Arg177Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001258610.1",
"strand": false,
"transcript": "NM_001271681.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 246,
"aa_ref": "R",
"aa_start": 177,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1549,
"cdna_start": 759,
"cds_end": null,
"cds_length": 741,
"cds_start": 529,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000612039.4",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.529C>A",
"hgvs_p": "p.Arg177Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000478165.1",
"strand": false,
"transcript": "ENST00000612039.4",
"transcript_support_level": 3
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 215,
"aa_ref": "R",
"aa_start": 146,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1386,
"cdna_start": 604,
"cds_end": null,
"cds_length": 648,
"cds_start": 436,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000872070.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.436C>A",
"hgvs_p": "p.Arg146Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542129.1",
"strand": false,
"transcript": "ENST00000872070.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 186,
"aa_ref": "R",
"aa_start": 117,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1332,
"cdna_start": 550,
"cds_end": null,
"cds_length": 561,
"cds_start": 349,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000872067.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.349C>A",
"hgvs_p": "p.Arg117Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000542125.1",
"strand": false,
"transcript": "ENST00000872067.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 155,
"aa_ref": "R",
"aa_start": 86,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1203,
"cdna_start": 416,
"cds_end": null,
"cds_length": 468,
"cds_start": 256,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000931948.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.256C>A",
"hgvs_p": "p.Arg86Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000602006.1",
"strand": false,
"transcript": "ENST00000931948.1",
"transcript_support_level": null
},
{
"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": 1341,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000446534.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "n.1309C>A",
"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": "ENST00000446534.1",
"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": 506,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000466127.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "n.468C>A",
"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": "ENST00000466127.1",
"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": 3149,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000478402.5",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "n.2360C>A",
"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": "ENST00000478402.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs876657403",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"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": "Pathogenic",
"phylop100way_score": 7.95,
"pos": 225921254,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.901,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_013328.4"
}
]
}