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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: 22-49903845-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=49903845&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 49903845,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_024105.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1460C>T",
"hgvs_p": "p.Pro487Leu",
"transcript": "NM_024105.4",
"protein_id": "NP_077010.1",
"transcript_support_level": null,
"aa_start": 487,
"aa_end": null,
"aa_length": 488,
"cds_start": 1460,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000330817.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024105.4"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1460C>T",
"hgvs_p": "p.Pro487Leu",
"transcript": "ENST00000330817.11",
"protein_id": "ENSP00000333813.5",
"transcript_support_level": 1,
"aa_start": 487,
"aa_end": null,
"aa_length": 488,
"cds_start": 1460,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_024105.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000330817.11"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1460C>T",
"hgvs_p": "p.Pro487Leu",
"transcript": "ENST00000905517.1",
"protein_id": "ENSP00000575576.1",
"transcript_support_level": null,
"aa_start": 487,
"aa_end": null,
"aa_length": 488,
"cds_start": 1460,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905517.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1460C>T",
"hgvs_p": "p.Pro487Leu",
"transcript": "ENST00000905518.1",
"protein_id": "ENSP00000575577.1",
"transcript_support_level": null,
"aa_start": 487,
"aa_end": null,
"aa_length": 488,
"cds_start": 1460,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905518.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1460C>T",
"hgvs_p": "p.Pro487Leu",
"transcript": "ENST00000930042.1",
"protein_id": "ENSP00000600101.1",
"transcript_support_level": null,
"aa_start": 487,
"aa_end": null,
"aa_length": 488,
"cds_start": 1460,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000930042.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1460C>T",
"hgvs_p": "p.Pro487Leu",
"transcript": "ENST00000967561.1",
"protein_id": "ENSP00000637620.1",
"transcript_support_level": null,
"aa_start": 487,
"aa_end": null,
"aa_length": 488,
"cds_start": 1460,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967561.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1412C>T",
"hgvs_p": "p.Pro471Leu",
"transcript": "ENST00000905519.1",
"protein_id": "ENSP00000575578.1",
"transcript_support_level": null,
"aa_start": 471,
"aa_end": null,
"aa_length": 472,
"cds_start": 1412,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905519.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1286C>T",
"hgvs_p": "p.Pro429Leu",
"transcript": "ENST00000905516.1",
"protein_id": "ENSP00000575575.1",
"transcript_support_level": null,
"aa_start": 429,
"aa_end": null,
"aa_length": 430,
"cds_start": 1286,
"cds_end": null,
"cds_length": 1293,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905516.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1259C>T",
"hgvs_p": "p.Pro420Leu",
"transcript": "ENST00000905520.1",
"protein_id": "ENSP00000575579.1",
"transcript_support_level": null,
"aa_start": 420,
"aa_end": null,
"aa_length": 421,
"cds_start": 1259,
"cds_end": null,
"cds_length": 1266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905520.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.478C>T",
"hgvs_p": "p.Arg160Cys",
"transcript": "ENST00000486602.1",
"protein_id": "ENSP00000420630.1",
"transcript_support_level": 3,
"aa_start": 160,
"aa_end": null,
"aa_length": 204,
"cds_start": 478,
"cds_end": null,
"cds_length": 615,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000486602.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1238+334C>T",
"hgvs_p": null,
"transcript": "XM_017028936.2",
"protein_id": "XP_016884425.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 447,
"cds_start": null,
"cds_end": null,
"cds_length": 1344,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017028936.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "c.1238+334C>T",
"hgvs_p": null,
"transcript": "XM_017028937.2",
"protein_id": "XP_016884426.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 441,
"cds_start": null,
"cds_end": null,
"cds_length": 1326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017028937.2"
},
{
"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.1618G>A",
"hgvs_p": null,
"transcript": "ENST00000610245.1",
"protein_id": null,
"transcript_support_level": 6,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000610245.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"hgvs_c": "n.*279C>T",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000492791.1"
}
],
"gene_symbol": "ALG12",
"gene_hgnc_id": 19358,
"dbsnp": "rs778688714",
"frequency_reference_population": 0.000052041967,
"hom_count_reference_population": 0,
"allele_count_reference_population": 84,
"gnomad_exomes_af": 0.0000560935,
"gnomad_genomes_af": 0.0000131373,
"gnomad_exomes_ac": 82,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.20371919870376587,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.17,
"revel_prediction": "Benign",
"alphamissense_score": 0.0728,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.887,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_024105.4",
"gene_symbol": "ALG12",
"hgnc_id": 19358,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1460C>T",
"hgvs_p": "p.Pro487Leu"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000610245.1",
"gene_symbol": "ENSG00000273192",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1618G>A",
"hgvs_p": null
}
],
"clinvar_disease": "ALG12-congenital disorder of glycosylation",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "ALG12-congenital disorder of glycosylation",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}