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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: 1-225920544-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=225920544&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "PYCR2",
"hgnc_id": 30262,
"hgvs_c": "c.874C>T",
"hgvs_p": "p.Leu292Leu",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_013328.4",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000255835",
"hgnc_id": null,
"hgvs_c": "c.575+664C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000432920.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate",
"acmg_score": -2,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.44,
"chr": "1",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.4399999976158142,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 320,
"aa_ref": "L",
"aa_start": 292,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1680,
"cdna_start": 1014,
"cds_end": null,
"cds_length": 963,
"cds_start": 874,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_013328.4",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.874C>T",
"hgvs_p": "p.Leu292Leu",
"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": "L",
"aa_end": null,
"aa_length": 320,
"aa_ref": "L",
"aa_start": 292,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1680,
"cdna_start": 1014,
"cds_end": null,
"cds_length": 963,
"cds_start": 874,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000343818.11",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.874C>T",
"hgvs_p": "p.Leu292Leu",
"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": null,
"aa_end": null,
"aa_length": 359,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1625,
"cdna_start": null,
"cds_end": null,
"cds_length": 1080,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000432920.2",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000255835",
"hgvs_c": "c.575+664C>T",
"hgvs_p": null,
"intron_rank": 5,
"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": "L",
"aa_end": null,
"aa_length": 319,
"aa_ref": "L",
"aa_start": 291,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2232,
"cdna_start": 1085,
"cds_end": null,
"cds_length": 960,
"cds_start": 871,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000872062.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.871C>T",
"hgvs_p": "p.Leu291Leu",
"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": "L",
"aa_end": null,
"aa_length": 319,
"aa_ref": "L",
"aa_start": 291,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1740,
"cdna_start": 1074,
"cds_end": null,
"cds_length": 960,
"cds_start": 871,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000872065.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.871C>T",
"hgvs_p": "p.Leu291Leu",
"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": "L",
"aa_end": null,
"aa_length": 318,
"aa_ref": "L",
"aa_start": 290,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1688,
"cdna_start": 1029,
"cds_end": null,
"cds_length": 957,
"cds_start": 868,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000931949.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.868C>T",
"hgvs_p": "p.Leu290Leu",
"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": "L",
"aa_end": null,
"aa_length": 297,
"aa_ref": "L",
"aa_start": 269,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1630,
"cdna_start": 965,
"cds_end": null,
"cds_length": 894,
"cds_start": 805,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000931947.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.805C>T",
"hgvs_p": "p.Leu269Leu",
"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": "L",
"aa_end": null,
"aa_length": 295,
"aa_ref": "L",
"aa_start": 267,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1603,
"cdna_start": 939,
"cds_end": null,
"cds_length": 888,
"cds_start": 799,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000872071.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.799C>T",
"hgvs_p": "p.Leu267Leu",
"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": "L",
"aa_end": null,
"aa_length": 289,
"aa_ref": "L",
"aa_start": 261,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1661,
"cdna_start": 995,
"cds_end": null,
"cds_length": 870,
"cds_start": 781,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000872063.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.781C>T",
"hgvs_p": "p.Leu261Leu",
"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": "L",
"aa_end": null,
"aa_length": 288,
"aa_ref": "L",
"aa_start": 260,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1617,
"cdna_start": 950,
"cds_end": null,
"cds_length": 867,
"cds_start": 778,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000954487.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.778C>T",
"hgvs_p": "p.Leu260Leu",
"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": "L",
"aa_end": null,
"aa_length": 288,
"aa_ref": "L",
"aa_start": 260,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1480,
"cdna_start": 815,
"cds_end": null,
"cds_length": 867,
"cds_start": 778,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000954488.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.778C>T",
"hgvs_p": "p.Leu260Leu",
"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": "L",
"aa_end": null,
"aa_length": 260,
"aa_ref": "L",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1523,
"cdna_start": 861,
"cds_end": null,
"cds_length": 783,
"cds_start": 694,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000872068.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.694C>T",
"hgvs_p": "p.Leu232Leu",
"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": "L",
"aa_end": null,
"aa_length": 246,
"aa_ref": "L",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1458,
"cdna_start": 792,
"cds_end": null,
"cds_length": 741,
"cds_start": 652,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001271681.2",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.652C>T",
"hgvs_p": "p.Leu218Leu",
"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": "L",
"aa_end": null,
"aa_length": 246,
"aa_ref": "L",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1549,
"cdna_start": 882,
"cds_end": null,
"cds_length": 741,
"cds_start": 652,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000612039.4",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.652C>T",
"hgvs_p": "p.Leu218Leu",
"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": "L",
"aa_end": null,
"aa_length": 215,
"aa_ref": "L",
"aa_start": 187,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1386,
"cdna_start": 727,
"cds_end": null,
"cds_length": 648,
"cds_start": 559,
"consequences": [
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000872070.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.559C>T",
"hgvs_p": "p.Leu187Leu",
"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": "L",
"aa_end": null,
"aa_length": 186,
"aa_ref": "L",
"aa_start": 158,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1332,
"cdna_start": 673,
"cds_end": null,
"cds_length": 561,
"cds_start": 472,
"consequences": [
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000872067.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Leu158Leu",
"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": "L",
"aa_end": null,
"aa_length": 155,
"aa_ref": "L",
"aa_start": 127,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1203,
"cdna_start": 539,
"cds_end": null,
"cds_length": 468,
"cds_start": 379,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000931948.1",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "c.379C>T",
"hgvs_p": "p.Leu127Leu",
"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": 3149,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000478402.5",
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"hgvs_c": "n.2483C>T",
"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": null,
"effect": "synonymous_variant",
"frequency_reference_population": 6.918165e-7,
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.91817e-7,
"gnomad_exomes_homalt": 0,
"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": "Likely benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.501,
"pos": 225920544,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"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"
}
]
}