← Back to variant description
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: X-47606966-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=47606966&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PP3",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SYN1",
"hgnc_id": 11494,
"hgvs_c": "c.506G>A",
"hgvs_p": "p.Arg169Gln",
"inheritance_mode": "XL",
"pathogenic_score": 1,
"score": -3,
"transcript": "NM_006950.3",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PP3",
"BS2"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000283743",
"hgnc_id": null,
"hgvs_c": "n.2962G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 1,
"score": -3,
"transcript": "ENST00000638776.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_score": -3,
"allele_count_reference_population": 18,
"alphamissense_prediction": null,
"alphamissense_score": 0.4983,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.62,
"chr": "X",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " X-linked 1, with variable learning disabilities and behavior disorders,Epilepsy,Inborn genetic diseases,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.7821813225746155,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 705,
"aa_ref": "R",
"aa_start": 169,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3210,
"cdna_start": 635,
"cds_end": null,
"cds_length": 2118,
"cds_start": 506,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_006950.3",
"gene_hgnc_id": 11494,
"gene_symbol": "SYN1",
"hgvs_c": "c.506G>A",
"hgvs_p": "p.Arg169Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000295987.13",
"protein_coding": true,
"protein_id": "NP_008881.2",
"strand": false,
"transcript": "NM_006950.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 705,
"aa_ref": "R",
"aa_start": 169,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3210,
"cdna_start": 635,
"cds_end": null,
"cds_length": 2118,
"cds_start": 506,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000295987.13",
"gene_hgnc_id": 11494,
"gene_symbol": "SYN1",
"hgvs_c": "c.506G>A",
"hgvs_p": "p.Arg169Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006950.3",
"protein_coding": true,
"protein_id": "ENSP00000295987.7",
"strand": false,
"transcript": "ENST00000295987.13",
"transcript_support_level": 2
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 669,
"aa_ref": "R",
"aa_start": 169,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3172,
"cdna_start": 635,
"cds_end": null,
"cds_length": 2010,
"cds_start": 506,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000340666.5",
"gene_hgnc_id": 11494,
"gene_symbol": "SYN1",
"hgvs_c": "c.506G>A",
"hgvs_p": "p.Arg169Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000343206.4",
"strand": false,
"transcript": "ENST00000340666.5",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 704,
"aa_ref": "R",
"aa_start": 169,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3204,
"cdna_start": 633,
"cds_end": null,
"cds_length": 2115,
"cds_start": 506,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000950906.1",
"gene_hgnc_id": 11494,
"gene_symbol": "SYN1",
"hgvs_c": "c.506G>A",
"hgvs_p": "p.Arg169Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000620965.1",
"strand": false,
"transcript": "ENST00000950906.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 680,
"aa_ref": "R",
"aa_start": 169,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3130,
"cdna_start": 636,
"cds_end": null,
"cds_length": 2043,
"cds_start": 506,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000950907.1",
"gene_hgnc_id": 11494,
"gene_symbol": "SYN1",
"hgvs_c": "c.506G>A",
"hgvs_p": "p.Arg169Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000620966.1",
"strand": false,
"transcript": "ENST00000950907.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 669,
"aa_ref": "R",
"aa_start": 169,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3172,
"cdna_start": 635,
"cds_end": null,
"cds_length": 2010,
"cds_start": 506,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_133499.2",
"gene_hgnc_id": 11494,
"gene_symbol": "SYN1",
"hgvs_c": "c.506G>A",
"hgvs_p": "p.Arg169Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_598006.1",
"strand": false,
"transcript": "NM_133499.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 147,
"aa_ref": "R",
"aa_start": 55,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 688,
"cdna_start": 165,
"cds_end": null,
"cds_length": 444,
"cds_start": 164,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000639776.1",
"gene_hgnc_id": 11494,
"gene_symbol": "SYN1",
"hgvs_c": "c.164G>A",
"hgvs_p": "p.Arg55Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000492521.1",
"strand": false,
"transcript": "ENST00000639776.1",
"transcript_support_level": 3
},
{
"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": 585,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000638337.1",
"gene_hgnc_id": 11494,
"gene_symbol": "SYN1",
"hgvs_c": "n.49G>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": "ENST00000638337.1",
"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": 3761,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 16,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000638776.2",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000283743",
"hgvs_c": "n.2962G>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": "ENST00000638776.2",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs775109362",
"effect": "missense_variant",
"frequency_reference_population": 0.00001490371,
"gene_hgnc_id": 11494,
"gene_symbol": "SYN1",
"gnomad_exomes_ac": 12,
"gnomad_exomes_af": 0.0000109316,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 6,
"gnomad_genomes_af": 0.0000545341,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 6,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not specified|Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders|Inborn genetic diseases|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.83,
"pos": 47606966,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.105,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_006950.3"
}
]
}