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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: 22-49904240-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=49904240&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 49904240,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000330817.11",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1177A>G",
"hgvs_p": "p.Ile393Val",
"transcript": "NM_024105.4",
"protein_id": "NP_077010.1",
"transcript_support_level": null,
"aa_start": 393,
"aa_end": null,
"aa_length": 488,
"cds_start": 1177,
"cds_end": null,
"cds_length": 1467,
"cdna_start": 1431,
"cdna_end": null,
"cdna_length": 5330,
"mane_select": "ENST00000330817.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1177A>G",
"hgvs_p": "p.Ile393Val",
"transcript": "ENST00000330817.11",
"protein_id": "ENSP00000333813.5",
"transcript_support_level": 1,
"aa_start": 393,
"aa_end": null,
"aa_length": 488,
"cds_start": 1177,
"cds_end": null,
"cds_length": 1467,
"cdna_start": 1431,
"cdna_end": null,
"cdna_length": 5330,
"mane_select": "NM_024105.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.382A>G",
"hgvs_p": "p.Ile128Val",
"transcript": "ENST00000486602.1",
"protein_id": "ENSP00000420630.1",
"transcript_support_level": 3,
"aa_start": 128,
"aa_end": null,
"aa_length": 204,
"cds_start": 382,
"cds_end": null,
"cds_length": 615,
"cdna_start": 383,
"cdna_end": null,
"cdna_length": 674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1177A>G",
"hgvs_p": "p.Ile393Val",
"transcript": "XM_017028936.2",
"protein_id": "XP_016884425.1",
"transcript_support_level": null,
"aa_start": 393,
"aa_end": null,
"aa_length": 447,
"cds_start": 1177,
"cds_end": null,
"cds_length": 1344,
"cdna_start": 1431,
"cdna_end": null,
"cdna_length": 2473,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1177A>G",
"hgvs_p": "p.Ile393Val",
"transcript": "XM_017028937.2",
"protein_id": "XP_016884426.1",
"transcript_support_level": null,
"aa_start": 393,
"aa_end": null,
"aa_length": 441,
"cds_start": 1177,
"cds_end": null,
"cds_length": 1326,
"cdna_start": 1431,
"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": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "n.584A>G",
"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
},
{
"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.2013T>C",
"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
}
],
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"dbsnp": "rs3922872",
"frequency_reference_population": 0.1138464,
"hom_count_reference_population": 11273,
"allele_count_reference_population": 183749,
"gnomad_exomes_af": 0.115872,
"gnomad_genomes_af": 0.0943875,
"gnomad_exomes_ac": 169387,
"gnomad_genomes_ac": 14362,
"gnomad_exomes_homalt": 10501,
"gnomad_genomes_homalt": 772,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.007071763277053833,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.257,
"revel_prediction": "Benign",
"alphamissense_score": 0.0863,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.4,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.02,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000330817.11",
"gene_symbol": "ALG12",
"hgnc_id": 19358,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1177A>G",
"hgvs_p": "p.Ile393Val"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000610245.1",
"gene_symbol": "ENSG00000273192",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.2013T>C",
"hgvs_p": null
}
],
"clinvar_disease": "ALG12-congenital disorder of glycosylation,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "not specified|ALG12-congenital disorder of glycosylation|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}