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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: 22-49904451-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=49904451&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 49904451,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000330817.11",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1048G>A",
"hgvs_p": "p.Gly350Arg",
"transcript": "NM_024105.4",
"protein_id": "NP_077010.1",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 488,
"cds_start": 1048,
"cds_end": null,
"cds_length": 1467,
"cdna_start": 1302,
"cdna_end": null,
"cdna_length": 5330,
"mane_select": "ENST00000330817.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1048G>A",
"hgvs_p": "p.Gly350Arg",
"transcript": "ENST00000330817.11",
"protein_id": "ENSP00000333813.5",
"transcript_support_level": 1,
"aa_start": 350,
"aa_end": null,
"aa_length": 488,
"cds_start": 1048,
"cds_end": null,
"cds_length": 1467,
"cdna_start": 1302,
"cdna_end": null,
"cdna_length": 5330,
"mane_select": "NM_024105.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.253G>A",
"hgvs_p": "p.Gly85Arg",
"transcript": "ENST00000486602.1",
"protein_id": "ENSP00000420630.1",
"transcript_support_level": 3,
"aa_start": 85,
"aa_end": null,
"aa_length": 204,
"cds_start": 253,
"cds_end": null,
"cds_length": 615,
"cdna_start": 254,
"cdna_end": null,
"cdna_length": 674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1048G>A",
"hgvs_p": "p.Gly350Arg",
"transcript": "XM_017028936.2",
"protein_id": "XP_016884425.1",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 447,
"cds_start": 1048,
"cds_end": null,
"cds_length": 1344,
"cdna_start": 1302,
"cdna_end": null,
"cdna_length": 2473,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1048G>A",
"hgvs_p": "p.Gly350Arg",
"transcript": "XM_017028937.2",
"protein_id": "XP_016884426.1",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 441,
"cds_start": 1048,
"cds_end": null,
"cds_length": 1326,
"cdna_start": 1302,
"cdna_end": null,
"cdna_length": 1683,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000273192",
"gene_hgnc_id": null,
"hgvs_c": "n.2224C>T",
"hgvs_p": null,
"transcript": "ENST00000610245.1",
"protein_id": null,
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2349,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "n.522-67G>A",
"hgvs_p": null,
"transcript": "ENST00000492791.1",
"protein_id": "ENSP00000417387.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 753,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"dbsnp": "rs377095724",
"frequency_reference_population": 0.000014870349,
"hom_count_reference_population": 0,
"allele_count_reference_population": 24,
"gnomad_exomes_af": 0.000015049,
"gnomad_genomes_af": 0.0000131525,
"gnomad_exomes_ac": 22,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8771296739578247,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.41,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7513,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.875,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.03,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000330817.11",
"gene_symbol": "ALG12",
"hgnc_id": 19358,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1048G>A",
"hgvs_p": "p.Gly350Arg"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000610245.1",
"gene_symbol": "ENSG00000273192",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.2224C>T",
"hgvs_p": null
}
],
"clinvar_disease": "ALG12-congenital disorder of glycosylation,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "ALG12-congenital disorder of glycosylation|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}