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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: 1-52397821-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=52397821&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PP3_Strong",
"PP5"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ORC1",
"hgnc_id": 8487,
"hgvs_c": "c.266T>C",
"hgvs_p": "p.Phe89Ser",
"inheritance_mode": "AR,AD",
"pathogenic_score": 5,
"score": 5,
"transcript": "NM_004153.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,PP5",
"acmg_score": 5,
"allele_count_reference_population": 7,
"alphamissense_prediction": null,
"alphamissense_score": 0.7619,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.36,
"chr": "1",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Meier-Gorlin syndrome 1,ORC1-related disorder,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9662742614746094,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 861,
"aa_ref": "F",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3121,
"cdna_start": 449,
"cds_end": null,
"cds_length": 2586,
"cds_start": 266,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_004153.4",
"gene_hgnc_id": 8487,
"gene_symbol": "ORC1",
"hgvs_c": "c.266T>C",
"hgvs_p": "p.Phe89Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000371568.8",
"protein_coding": true,
"protein_id": "NP_004144.2",
"strand": false,
"transcript": "NM_004153.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 861,
"aa_ref": "F",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3121,
"cdna_start": 449,
"cds_end": null,
"cds_length": 2586,
"cds_start": 266,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000371568.8",
"gene_hgnc_id": 8487,
"gene_symbol": "ORC1",
"hgvs_c": "c.266T>C",
"hgvs_p": "p.Phe89Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004153.4",
"protein_coding": true,
"protein_id": "ENSP00000360623.3",
"strand": false,
"transcript": "ENST00000371568.8",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 861,
"aa_ref": "F",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3080,
"cdna_start": 410,
"cds_end": null,
"cds_length": 2586,
"cds_start": 266,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000371566.1",
"gene_hgnc_id": 8487,
"gene_symbol": "ORC1",
"hgvs_c": "c.266T>C",
"hgvs_p": "p.Phe89Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000360621.1",
"strand": false,
"transcript": "ENST00000371566.1",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 861,
"aa_ref": "F",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3118,
"cdna_start": 446,
"cds_end": null,
"cds_length": 2586,
"cds_start": 266,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001190818.2",
"gene_hgnc_id": 8487,
"gene_symbol": "ORC1",
"hgvs_c": "c.266T>C",
"hgvs_p": "p.Phe89Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001177747.1",
"strand": false,
"transcript": "NM_001190818.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 861,
"aa_ref": "F",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3291,
"cdna_start": 621,
"cds_end": null,
"cds_length": 2586,
"cds_start": 266,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000959732.1",
"gene_hgnc_id": 8487,
"gene_symbol": "ORC1",
"hgvs_c": "c.266T>C",
"hgvs_p": "p.Phe89Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629791.1",
"strand": false,
"transcript": "ENST00000959732.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 860,
"aa_ref": "F",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3133,
"cdna_start": 464,
"cds_end": null,
"cds_length": 2583,
"cds_start": 266,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000921464.1",
"gene_hgnc_id": 8487,
"gene_symbol": "ORC1",
"hgvs_c": "c.266T>C",
"hgvs_p": "p.Phe89Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000591523.1",
"strand": false,
"transcript": "ENST00000921464.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 856,
"aa_ref": "F",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3106,
"cdna_start": 449,
"cds_end": null,
"cds_length": 2571,
"cds_start": 266,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001190819.2",
"gene_hgnc_id": 8487,
"gene_symbol": "ORC1",
"hgvs_c": "c.266T>C",
"hgvs_p": "p.Phe89Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001177748.1",
"strand": false,
"transcript": "NM_001190819.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 856,
"aa_ref": "F",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3095,
"cdna_start": 443,
"cds_end": null,
"cds_length": 2571,
"cds_start": 266,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000852389.1",
"gene_hgnc_id": 8487,
"gene_symbol": "ORC1",
"hgvs_c": "c.266T>C",
"hgvs_p": "p.Phe89Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522448.1",
"strand": false,
"transcript": "ENST00000852389.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 825,
"aa_ref": "F",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3880,
"cdna_start": 497,
"cds_end": null,
"cds_length": 2478,
"cds_start": 266,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000921462.1",
"gene_hgnc_id": 8487,
"gene_symbol": "ORC1",
"hgvs_c": "c.266T>C",
"hgvs_p": "p.Phe89Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000591521.1",
"strand": false,
"transcript": "ENST00000921462.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 825,
"aa_ref": "F",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3391,
"cdna_start": 492,
"cds_end": null,
"cds_length": 2478,
"cds_start": 266,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000921463.1",
"gene_hgnc_id": 8487,
"gene_symbol": "ORC1",
"hgvs_c": "c.266T>C",
"hgvs_p": "p.Phe89Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000591522.1",
"strand": false,
"transcript": "ENST00000921463.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 861,
"aa_ref": "F",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3114,
"cdna_start": 442,
"cds_end": null,
"cds_length": 2586,
"cds_start": 266,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_047421674.1",
"gene_hgnc_id": 8487,
"gene_symbol": "ORC1",
"hgvs_c": "c.266T>C",
"hgvs_p": "p.Phe89Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047277630.1",
"strand": false,
"transcript": "XM_047421674.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 825,
"aa_ref": "F",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3013,
"cdna_start": 449,
"cds_end": null,
"cds_length": 2478,
"cds_start": 266,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_017001388.3",
"gene_hgnc_id": 8487,
"gene_symbol": "ORC1",
"hgvs_c": "c.266T>C",
"hgvs_p": "p.Phe89Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016856877.1",
"strand": false,
"transcript": "XM_017001388.3",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 825,
"aa_ref": "F",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3010,
"cdna_start": 446,
"cds_end": null,
"cds_length": 2478,
"cds_start": 266,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_047421680.1",
"gene_hgnc_id": 8487,
"gene_symbol": "ORC1",
"hgvs_c": "c.266T>C",
"hgvs_p": "p.Phe89Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047277636.1",
"strand": false,
"transcript": "XM_047421680.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs387906827",
"effect": "missense_variant",
"frequency_reference_population": 0.0000043366476,
"gene_hgnc_id": 8487,
"gene_symbol": "ORC1",
"gnomad_exomes_ac": 6,
"gnomad_exomes_af": 0.00000410427,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.0000065678,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Meier-Gorlin syndrome 1|ORC1-related disorder|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 3.911,
"pos": 52397821,
"ref": "A",
"revel_prediction": "Pathogenic",
"revel_score": 0.93,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_004153.4"
}
]
}