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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: 1-225920494-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=225920494&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 21,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "PYCR2",
"hgnc_id": 30262,
"hgvs_c": "c.924C>G",
"hgvs_p": "p.Leu308Leu",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -21,
"transcript": "NM_013328.4",
"verdict": "Benign"
},
{
"benign_score": 16,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000255835",
"hgnc_id": null,
"hgvs_c": "c.575+714C>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -16,
"transcript": "ENST00000432920.2",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_score": -21,
"allele_count_reference_population": 878,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.66,
"chr": "1",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": "Hypomyelinating leukodystrophy 10,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.6600000262260437,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 320,
"aa_ref": "L",
"aa_start": 308,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1680,
"cdna_start": 1064,
"cds_end": null,
"cds_length": 963,
"cds_start": 924,
"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.924C>G",
"hgvs_p": "p.Leu308Leu",
"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": 308,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1680,
"cdna_start": 1064,
"cds_end": null,
"cds_length": 963,
"cds_start": 924,
"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.924C>G",
"hgvs_p": "p.Leu308Leu",
"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+714C>G",
"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": 307,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2232,
"cdna_start": 1135,
"cds_end": null,
"cds_length": 960,
"cds_start": 921,
"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.921C>G",
"hgvs_p": "p.Leu307Leu",
"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": 307,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1740,
"cdna_start": 1124,
"cds_end": null,
"cds_length": 960,
"cds_start": 921,
"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.921C>G",
"hgvs_p": "p.Leu307Leu",
"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": 306,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1688,
"cdna_start": 1079,
"cds_end": null,
"cds_length": 957,
"cds_start": 918,
"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.918C>G",
"hgvs_p": "p.Leu306Leu",
"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": 285,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1630,
"cdna_start": 1015,
"cds_end": null,
"cds_length": 894,
"cds_start": 855,
"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.855C>G",
"hgvs_p": "p.Leu285Leu",
"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": 283,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1603,
"cdna_start": 989,
"cds_end": null,
"cds_length": 888,
"cds_start": 849,
"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.849C>G",
"hgvs_p": "p.Leu283Leu",
"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": 277,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1661,
"cdna_start": 1045,
"cds_end": null,
"cds_length": 870,
"cds_start": 831,
"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.831C>G",
"hgvs_p": "p.Leu277Leu",
"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": 276,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1617,
"cdna_start": 1000,
"cds_end": null,
"cds_length": 867,
"cds_start": 828,
"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.828C>G",
"hgvs_p": "p.Leu276Leu",
"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": 276,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1480,
"cdna_start": 865,
"cds_end": null,
"cds_length": 867,
"cds_start": 828,
"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.828C>G",
"hgvs_p": "p.Leu276Leu",
"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": 248,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1523,
"cdna_start": 911,
"cds_end": null,
"cds_length": 783,
"cds_start": 744,
"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.744C>G",
"hgvs_p": "p.Leu248Leu",
"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": 234,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1458,
"cdna_start": 842,
"cds_end": null,
"cds_length": 741,
"cds_start": 702,
"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.702C>G",
"hgvs_p": "p.Leu234Leu",
"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": 234,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1549,
"cdna_start": 932,
"cds_end": null,
"cds_length": 741,
"cds_start": 702,
"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.702C>G",
"hgvs_p": "p.Leu234Leu",
"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": 203,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1386,
"cdna_start": 777,
"cds_end": null,
"cds_length": 648,
"cds_start": 609,
"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.609C>G",
"hgvs_p": "p.Leu203Leu",
"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": 174,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1332,
"cdna_start": 723,
"cds_end": null,
"cds_length": 561,
"cds_start": 522,
"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.522C>G",
"hgvs_p": "p.Leu174Leu",
"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": 143,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1203,
"cdna_start": 589,
"cds_end": null,
"cds_length": 468,
"cds_start": 429,
"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.429C>G",
"hgvs_p": "p.Leu143Leu",
"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.2533C>G",
"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": "rs181648767",
"effect": "synonymous_variant",
"frequency_reference_population": 0.000586435,
"gene_hgnc_id": 30262,
"gene_symbol": "PYCR2",
"gnomad_exomes_ac": 739,
"gnomad_exomes_af": 0.00054948,
"gnomad_exomes_homalt": 6,
"gnomad_genomes_ac": 139,
"gnomad_genomes_af": 0.000912828,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 7,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "not provided|not specified|Hypomyelinating leukodystrophy 10",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.373,
"pos": 225920494,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_013328.4"
}
]
}