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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-112791832-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=112791832&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"effects": [
"missense_variant",
"splice_region_variant"
],
"gene_symbol": "AMOT",
"hgnc_id": 17810,
"hgvs_c": "c.1926G>C",
"hgvs_p": "p.Gln642His",
"inheritance_mode": "",
"pathogenic_score": 8,
"score": 8,
"transcript": "NM_001113490.2",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Moderate",
"acmg_score": 8,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.8364,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.11,
"chr": "X",
"clinvar_classification": "Likely pathogenic",
"clinvar_disease": "Cerebral visual impairment and intellectual disability",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.6444029808044434,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1084,
"aa_ref": "Q",
"aa_start": 642,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7613,
"cdna_start": 2594,
"cds_end": null,
"cds_length": 3255,
"cds_start": 1926,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001113490.2",
"gene_hgnc_id": 17810,
"gene_symbol": "AMOT",
"hgvs_c": "c.1926G>C",
"hgvs_p": "p.Gln642His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000371959.9",
"protein_coding": true,
"protein_id": "NP_001106962.1",
"strand": false,
"transcript": "NM_001113490.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1084,
"aa_ref": "Q",
"aa_start": 642,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7613,
"cdna_start": 2594,
"cds_end": null,
"cds_length": 3255,
"cds_start": 1926,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000371959.9",
"gene_hgnc_id": 17810,
"gene_symbol": "AMOT",
"hgvs_c": "c.1926G>C",
"hgvs_p": "p.Gln642His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001113490.2",
"protein_coding": true,
"protein_id": "ENSP00000361027.3",
"strand": false,
"transcript": "ENST00000371959.9",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 852,
"aa_ref": "Q",
"aa_start": 410,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2720,
"cdna_start": 1336,
"cds_end": null,
"cds_length": 2559,
"cds_start": 1230,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 11,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000371962.5",
"gene_hgnc_id": 17810,
"gene_symbol": "AMOT",
"hgvs_c": "c.1230G>C",
"hgvs_p": "p.Gln410His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000361030.1",
"strand": false,
"transcript": "ENST00000371962.5",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 675,
"aa_ref": "Q",
"aa_start": 233,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6888,
"cdna_start": 1495,
"cds_end": null,
"cds_length": 2028,
"cds_start": 699,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000304758.5",
"gene_hgnc_id": 17810,
"gene_symbol": "AMOT",
"hgvs_c": "c.699G>C",
"hgvs_p": "p.Gln233His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000305557.1",
"strand": false,
"transcript": "ENST00000304758.5",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1084,
"aa_ref": "Q",
"aa_start": 642,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7687,
"cdna_start": 2668,
"cds_end": null,
"cds_length": 3255,
"cds_start": 1926,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001386998.1",
"gene_hgnc_id": 17810,
"gene_symbol": "AMOT",
"hgvs_c": "c.1926G>C",
"hgvs_p": "p.Gln642His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001373927.1",
"strand": false,
"transcript": "NM_001386998.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1084,
"aa_ref": "Q",
"aa_start": 642,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7823,
"cdna_start": 2804,
"cds_end": null,
"cds_length": 3255,
"cds_start": 1926,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001386999.1",
"gene_hgnc_id": 17810,
"gene_symbol": "AMOT",
"hgvs_c": "c.1926G>C",
"hgvs_p": "p.Gln642His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001373928.1",
"strand": false,
"transcript": "NM_001386999.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 675,
"aa_ref": "Q",
"aa_start": 233,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6530,
"cdna_start": 1511,
"cds_end": null,
"cds_length": 2028,
"cds_start": 699,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_133265.5",
"gene_hgnc_id": 17810,
"gene_symbol": "AMOT",
"hgvs_c": "c.699G>C",
"hgvs_p": "p.Gln233His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_573572.1",
"strand": false,
"transcript": "NM_133265.5",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 597,
"aa_ref": "Q",
"aa_start": 410,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2462,
"cdna_start": 1384,
"cds_end": null,
"cds_length": 1794,
"cds_start": 1230,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000371958.1",
"gene_hgnc_id": 17810,
"gene_symbol": "AMOT",
"hgvs_c": "c.1230G>C",
"hgvs_p": "p.Gln410His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000361026.1",
"strand": false,
"transcript": "ENST00000371958.1",
"transcript_support_level": 5
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1084,
"aa_ref": "Q",
"aa_start": 642,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7721,
"cdna_start": 2702,
"cds_end": null,
"cds_length": 3255,
"cds_start": 1926,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047441856.1",
"gene_hgnc_id": 17810,
"gene_symbol": "AMOT",
"hgvs_c": "c.1926G>C",
"hgvs_p": "p.Gln642His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047297812.1",
"strand": false,
"transcript": "XM_047441856.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1084,
"aa_ref": "Q",
"aa_start": 642,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13559,
"cdna_start": 8540,
"cds_end": null,
"cds_length": 3255,
"cds_start": 1926,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_047441857.1",
"gene_hgnc_id": 17810,
"gene_symbol": "AMOT",
"hgvs_c": "c.1926G>C",
"hgvs_p": "p.Gln642His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047297813.1",
"strand": false,
"transcript": "XM_047441857.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 675,
"aa_ref": "Q",
"aa_start": 233,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6187,
"cdna_start": 1168,
"cds_end": null,
"cds_length": 2028,
"cds_start": 699,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 11,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_005262090.1",
"gene_hgnc_id": 17810,
"gene_symbol": "AMOT",
"hgvs_c": "c.699G>C",
"hgvs_p": "p.Gln233His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005262147.1",
"strand": false,
"transcript": "XM_005262090.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.99999577061468,
"dbsnp": "rs869312862",
"effect": "missense_variant,splice_region_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 17810,
"gene_symbol": "AMOT",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"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 pathogenic",
"phenotype_combined": "Cerebral visual impairment and intellectual disability",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.038,
"pos": 112791832,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.265,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.9980000257492065,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.98,
"transcript": "NM_001113490.2"
}
]
}