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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: X-108072742-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=108072742&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "VSIG1",
"hgnc_id": 28675,
"hgvs_c": "c.586T>C",
"hgvs_p": "p.Ser196Pro",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_001170553.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_score": -4,
"allele_count_reference_population": 11,
"alphamissense_prediction": null,
"alphamissense_score": 0.82,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.43,
"chr": "X",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.6813294887542725,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 387,
"aa_ref": "S",
"aa_start": 160,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3033,
"cdna_start": 544,
"cds_end": null,
"cds_length": 1164,
"cds_start": 478,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_182607.5",
"gene_hgnc_id": 28675,
"gene_symbol": "VSIG1",
"hgvs_c": "c.478T>C",
"hgvs_p": "p.Ser160Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000217957.10",
"protein_coding": true,
"protein_id": "NP_872413.1",
"strand": true,
"transcript": "NM_182607.5",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 387,
"aa_ref": "S",
"aa_start": 160,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3033,
"cdna_start": 544,
"cds_end": null,
"cds_length": 1164,
"cds_start": 478,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000217957.10",
"gene_hgnc_id": 28675,
"gene_symbol": "VSIG1",
"hgvs_c": "c.478T>C",
"hgvs_p": "p.Ser160Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_182607.5",
"protein_coding": true,
"protein_id": "ENSP00000217957.3",
"strand": true,
"transcript": "ENST00000217957.10",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 423,
"aa_ref": "S",
"aa_start": 196,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3141,
"cdna_start": 652,
"cds_end": null,
"cds_length": 1272,
"cds_start": 586,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001170553.2",
"gene_hgnc_id": 28675,
"gene_symbol": "VSIG1",
"hgvs_c": "c.586T>C",
"hgvs_p": "p.Ser196Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001164024.1",
"strand": true,
"transcript": "NM_001170553.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 423,
"aa_ref": "S",
"aa_start": 196,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3236,
"cdna_start": 747,
"cds_end": null,
"cds_length": 1272,
"cds_start": 586,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000415430.7",
"gene_hgnc_id": 28675,
"gene_symbol": "VSIG1",
"hgvs_c": "c.586T>C",
"hgvs_p": "p.Ser196Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000402219.3",
"strand": true,
"transcript": "ENST00000415430.7",
"transcript_support_level": 2
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 449,
"aa_ref": "S",
"aa_start": 222,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3219,
"cdna_start": 730,
"cds_end": null,
"cds_length": 1350,
"cds_start": 664,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_005262127.5",
"gene_hgnc_id": 28675,
"gene_symbol": "VSIG1",
"hgvs_c": "c.664T>C",
"hgvs_p": "p.Ser222Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005262184.1",
"strand": true,
"transcript": "XM_005262127.5",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 442,
"aa_ref": "S",
"aa_start": 215,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3204,
"cdna_start": 715,
"cds_end": null,
"cds_length": 1329,
"cds_start": 643,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_011530936.3",
"gene_hgnc_id": 28675,
"gene_symbol": "VSIG1",
"hgvs_c": "c.643T>C",
"hgvs_p": "p.Ser215Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011529238.1",
"strand": true,
"transcript": "XM_011530936.3",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 413,
"aa_ref": "S",
"aa_start": 186,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3111,
"cdna_start": 622,
"cds_end": null,
"cds_length": 1242,
"cds_start": 556,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_047442072.1",
"gene_hgnc_id": 28675,
"gene_symbol": "VSIG1",
"hgvs_c": "c.556T>C",
"hgvs_p": "p.Ser186Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047298028.1",
"strand": true,
"transcript": "XM_047442072.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 380,
"aa_ref": "S",
"aa_start": 153,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3018,
"cdna_start": 529,
"cds_end": null,
"cds_length": 1143,
"cds_start": 457,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_047442073.1",
"gene_hgnc_id": 28675,
"gene_symbol": "VSIG1",
"hgvs_c": "c.457T>C",
"hgvs_p": "p.Ser153Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047298029.1",
"strand": true,
"transcript": "XM_047442073.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 419,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000485533.1",
"gene_hgnc_id": 28675,
"gene_symbol": "VSIG1",
"hgvs_c": "n.314T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000485533.1",
"transcript_support_level": 5
},
{
"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": 641,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000479635.1",
"gene_hgnc_id": 28675,
"gene_symbol": "VSIG1",
"hgvs_c": "n.-54T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000479635.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1440907821",
"effect": "missense_variant",
"frequency_reference_population": 0.000009099814,
"gene_hgnc_id": 28675,
"gene_symbol": "VSIG1",
"gnomad_exomes_ac": 7,
"gnomad_exomes_af": 0.00000637769,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.0000359583,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 5,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.035,
"pos": 108072742,
"ref": "T",
"revel_prediction": "Benign",
"revel_score": 0.172,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001170553.2"
}
]
}