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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: 3-121988395-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=121988395&ref=G&alt=C&genome=hg38&allGenes=true"
API Response
json
{
"variants": [
{
"chr": "3",
"pos": 121988395,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001199799.2",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ILDR1",
"gene_hgnc_id": 28741,
"hgvs_c": "c.1613C>G",
"hgvs_p": "p.Ser538Cys",
"transcript": "NM_001199799.2",
"protein_id": "NP_001186728.1",
"transcript_support_level": null,
"aa_start": 538,
"aa_end": null,
"aa_length": 546,
"cds_start": 1613,
"cds_end": null,
"cds_length": 1641,
"cdna_start": 1783,
"cdna_end": null,
"cdna_length": 2855,
"mane_select": "ENST00000344209.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ILDR1",
"gene_hgnc_id": 28741,
"hgvs_c": "c.1613C>G",
"hgvs_p": "p.Ser538Cys",
"transcript": "ENST00000344209.10",
"protein_id": "ENSP00000345667.5",
"transcript_support_level": 1,
"aa_start": 538,
"aa_end": null,
"aa_length": 546,
"cds_start": 1613,
"cds_end": null,
"cds_length": 1641,
"cdna_start": 1783,
"cdna_end": null,
"cdna_length": 2855,
"mane_select": "NM_001199799.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ILDR1",
"gene_hgnc_id": 28741,
"hgvs_c": "c.1481C>G",
"hgvs_p": "p.Ser494Cys",
"transcript": "ENST00000273691.7",
"protein_id": "ENSP00000273691.3",
"transcript_support_level": 1,
"aa_start": 494,
"aa_end": null,
"aa_length": 502,
"cds_start": 1481,
"cds_end": null,
"cds_length": 1509,
"cdna_start": 1587,
"cdna_end": null,
"cdna_length": 2659,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ILDR1",
"gene_hgnc_id": 28741,
"hgvs_c": "c.1346C>G",
"hgvs_p": "p.Ser449Cys",
"transcript": "ENST00000393631.5",
"protein_id": "ENSP00000377251.1",
"transcript_support_level": 1,
"aa_start": 449,
"aa_end": null,
"aa_length": 457,
"cds_start": 1346,
"cds_end": null,
"cds_length": 1374,
"cdna_start": 1391,
"cdna_end": null,
"cdna_length": 1456,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ILDR1",
"gene_hgnc_id": 28741,
"hgvs_c": "n.1563C>G",
"hgvs_p": null,
"transcript": "ENST00000460554.2",
"protein_id": null,
"transcript_support_level": 1,
"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": 1612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ILDR1",
"gene_hgnc_id": 28741,
"hgvs_c": "c.1481C>G",
"hgvs_p": "p.Ser494Cys",
"transcript": "NM_175924.4",
"protein_id": "NP_787120.1",
"transcript_support_level": null,
"aa_start": 494,
"aa_end": null,
"aa_length": 502,
"cds_start": 1481,
"cds_end": null,
"cds_length": 1509,
"cdna_start": 1651,
"cdna_end": null,
"cdna_length": 2723,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ILDR1",
"gene_hgnc_id": 28741,
"hgvs_c": "c.1346C>G",
"hgvs_p": "p.Ser449Cys",
"transcript": "NM_001199800.2",
"protein_id": "NP_001186729.1",
"transcript_support_level": null,
"aa_start": 449,
"aa_end": null,
"aa_length": 457,
"cds_start": 1346,
"cds_end": null,
"cds_length": 1374,
"cdna_start": 1516,
"cdna_end": null,
"cdna_length": 2588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ILDR1",
"gene_hgnc_id": 28741,
"hgvs_c": "c.1517C>G",
"hgvs_p": "p.Ser506Cys",
"transcript": "XM_005247389.5",
"protein_id": "XP_005247446.1",
"transcript_support_level": null,
"aa_start": 506,
"aa_end": null,
"aa_length": 514,
"cds_start": 1517,
"cds_end": null,
"cds_length": 1545,
"cdna_start": 2097,
"cdna_end": null,
"cdna_length": 3169,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ILDR1",
"gene_hgnc_id": 28741,
"hgvs_c": "c.1208C>G",
"hgvs_p": "p.Ser403Cys",
"transcript": "XM_047448044.1",
"protein_id": "XP_047304000.1",
"transcript_support_level": null,
"aa_start": 403,
"aa_end": null,
"aa_length": 411,
"cds_start": 1208,
"cds_end": null,
"cds_length": 1236,
"cdna_start": 2791,
"cdna_end": null,
"cdna_length": 3863,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ILDR1",
"gene_hgnc_id": 28741,
"hgvs_c": "c.1572C>G",
"hgvs_p": "p.Leu524Leu",
"transcript": "XM_011512738.3",
"protein_id": "XP_011511040.1",
"transcript_support_level": null,
"aa_start": 524,
"aa_end": null,
"aa_length": 525,
"cds_start": 1572,
"cds_end": null,
"cds_length": 1578,
"cdna_start": 1742,
"cdna_end": null,
"cdna_length": 2814,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ILDR1",
"gene_hgnc_id": 28741,
"hgvs_c": "c.1440C>G",
"hgvs_p": "p.Leu480Leu",
"transcript": "XM_047448043.1",
"protein_id": "XP_047303999.1",
"transcript_support_level": null,
"aa_start": 480,
"aa_end": null,
"aa_length": 481,
"cds_start": 1440,
"cds_end": null,
"cds_length": 1446,
"cdna_start": 1610,
"cdna_end": null,
"cdna_length": 2682,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC101927010",
"gene_hgnc_id": null,
"hgvs_c": "n.217G>C",
"hgvs_p": null,
"transcript": "XR_241555.5",
"protein_id": null,
"transcript_support_level": null,
"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": 2213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ILDR1",
"gene_hgnc_id": 28741,
"hgvs_c": "n.*796C>G",
"hgvs_p": null,
"transcript": "ENST00000642615.1",
"protein_id": "ENSP00000495499.1",
"transcript_support_level": null,
"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": 1704,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ILDR1",
"gene_hgnc_id": 28741,
"dbsnp": "rs568713946",
"frequency_reference_population": 0.000019832563,
"hom_count_reference_population": 0,
"allele_count_reference_population": 32,
"gnomad_exomes_af": 0.0000164221,
"gnomad_genomes_af": 0.0000526094,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5717740058898926,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.451,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2536,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.13,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.262,
"phylop100way_prediction": "Uncertain_significance",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001199799.2",
"gene_symbol": "ILDR1",
"hgnc_id": 28741,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1613C>G",
"hgvs_p": "p.Ser538Cys"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "XR_241555.5",
"gene_symbol": "LOC101927010",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.217G>C",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Inborn genetic diseases|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}