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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: 22-49910602-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=49910602&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ALG12",
"hgnc_id": 19358,
"hgvs_c": "c.301G>A",
"hgvs_p": "p.Gly101Arg",
"inheritance_mode": "AR",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_024105.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Moderate,PP5_Very_Strong",
"acmg_score": 12,
"allele_count_reference_population": 22,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.8753,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.26,
"chr": "22",
"clinvar_classification": "Likely pathogenic",
"clinvar_disease": "ALG12-congenital disorder of glycosylation,ALG12-related disorder,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:3",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9120608568191528,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 488,
"aa_ref": "G",
"aa_start": 101,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5330,
"cdna_start": 555,
"cds_end": null,
"cds_length": 1467,
"cds_start": 301,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_024105.4",
"gene_hgnc_id": 19358,
"gene_symbol": "ALG12",
"hgvs_c": "c.301G>A",
"hgvs_p": "p.Gly101Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000330817.11",
"protein_coding": true,
"protein_id": "NP_077010.1",
"strand": false,
"transcript": "NM_024105.4",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 488,
"aa_ref": "G",
"aa_start": 101,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5330,
"cdna_start": 555,
"cds_end": null,
"cds_length": 1467,
"cds_start": 301,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000330817.11",
"gene_hgnc_id": 19358,
"gene_symbol": "ALG12",
"hgvs_c": "c.301G>A",
"hgvs_p": "p.Gly101Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_024105.4",
"protein_coding": true,
"protein_id": "ENSP00000333813.5",
"strand": false,
"transcript": "ENST00000330817.11",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 488,
"aa_ref": "G",
"aa_start": 101,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2372,
"cdna_start": 586,
"cds_end": null,
"cds_length": 1467,
"cds_start": 301,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000905517.1",
"gene_hgnc_id": 19358,
"gene_symbol": "ALG12",
"hgvs_c": "c.301G>A",
"hgvs_p": "p.Gly101Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000575576.1",
"strand": false,
"transcript": "ENST00000905517.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 488,
"aa_ref": "G",
"aa_start": 101,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3075,
"cdna_start": 1275,
"cds_end": null,
"cds_length": 1467,
"cds_start": 301,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000905518.1",
"gene_hgnc_id": 19358,
"gene_symbol": "ALG12",
"hgvs_c": "c.301G>A",
"hgvs_p": "p.Gly101Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000575577.1",
"strand": false,
"transcript": "ENST00000905518.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 488,
"aa_ref": "G",
"aa_start": 101,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6560,
"cdna_start": 4772,
"cds_end": null,
"cds_length": 1467,
"cds_start": 301,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000930042.1",
"gene_hgnc_id": 19358,
"gene_symbol": "ALG12",
"hgvs_c": "c.301G>A",
"hgvs_p": "p.Gly101Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600101.1",
"strand": false,
"transcript": "ENST00000930042.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 488,
"aa_ref": "G",
"aa_start": 101,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2470,
"cdna_start": 684,
"cds_end": null,
"cds_length": 1467,
"cds_start": 301,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000967561.1",
"gene_hgnc_id": 19358,
"gene_symbol": "ALG12",
"hgvs_c": "c.301G>A",
"hgvs_p": "p.Gly101Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000637620.1",
"strand": false,
"transcript": "ENST00000967561.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 472,
"aa_ref": "G",
"aa_start": 101,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2267,
"cdna_start": 527,
"cds_end": null,
"cds_length": 1419,
"cds_start": 301,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000905519.1",
"gene_hgnc_id": 19358,
"gene_symbol": "ALG12",
"hgvs_c": "c.301G>A",
"hgvs_p": "p.Gly101Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000575578.1",
"strand": false,
"transcript": "ENST00000905519.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 421,
"aa_ref": "G",
"aa_start": 101,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2025,
"cdna_start": 441,
"cds_end": null,
"cds_length": 1266,
"cds_start": 301,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000905520.1",
"gene_hgnc_id": 19358,
"gene_symbol": "ALG12",
"hgvs_c": "c.301G>A",
"hgvs_p": "p.Gly101Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000575579.1",
"strand": false,
"transcript": "ENST00000905520.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 447,
"aa_ref": "G",
"aa_start": 101,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2473,
"cdna_start": 555,
"cds_end": null,
"cds_length": 1344,
"cds_start": 301,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_017028936.2",
"gene_hgnc_id": 19358,
"gene_symbol": "ALG12",
"hgvs_c": "c.301G>A",
"hgvs_p": "p.Gly101Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016884425.1",
"strand": false,
"transcript": "XM_017028936.2",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 441,
"aa_ref": "G",
"aa_start": 101,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1683,
"cdna_start": 555,
"cds_end": null,
"cds_length": 1326,
"cds_start": 301,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_017028937.2",
"gene_hgnc_id": 19358,
"gene_symbol": "ALG12",
"hgvs_c": "c.301G>A",
"hgvs_p": "p.Gly101Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016884426.1",
"strand": false,
"transcript": "XM_017028937.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 430,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2189,
"cdna_start": null,
"cds_end": null,
"cds_length": 1293,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000905516.1",
"gene_hgnc_id": 19358,
"gene_symbol": "ALG12",
"hgvs_c": "c.296-514G>A",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000575575.1",
"strand": false,
"transcript": "ENST00000905516.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs121907933",
"effect": "missense_variant",
"frequency_reference_population": 0.000013630545,
"gene_hgnc_id": 19358,
"gene_symbol": "ALG12",
"gnomad_exomes_ac": 19,
"gnomad_exomes_af": 0.0000129979,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.000019705,
"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": "Likely pathogenic",
"phenotype_combined": "ALG12-congenital disorder of glycosylation|not provided|ALG12-related disorder",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.463,
"pos": 49910602,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.727,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.03999999910593033,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.04,
"transcript": "NM_024105.4"
}
]
}