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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: 1-30874339-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=30874339&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 30874339,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_014654.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDC3",
"gene_hgnc_id": 10660,
"hgvs_c": "c.1120C>A",
"hgvs_p": "p.Leu374Met",
"transcript": "NM_014654.4",
"protein_id": "NP_055469.3",
"transcript_support_level": null,
"aa_start": 374,
"aa_end": null,
"aa_length": 442,
"cds_start": 1120,
"cds_end": null,
"cds_length": 1329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000339394.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014654.4"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDC3",
"gene_hgnc_id": 10660,
"hgvs_c": "c.1120C>A",
"hgvs_p": "p.Leu374Met",
"transcript": "ENST00000339394.7",
"protein_id": "ENSP00000344468.6",
"transcript_support_level": 1,
"aa_start": 374,
"aa_end": null,
"aa_length": 442,
"cds_start": 1120,
"cds_end": null,
"cds_length": 1329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_014654.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000339394.7"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDC3",
"gene_hgnc_id": 10660,
"hgvs_c": "c.946C>A",
"hgvs_p": "p.Leu316Met",
"transcript": "ENST00000336798.11",
"protein_id": "ENSP00000338346.7",
"transcript_support_level": 1,
"aa_start": 316,
"aa_end": null,
"aa_length": 384,
"cds_start": 946,
"cds_end": null,
"cds_length": 1155,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000336798.11"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDC3",
"gene_hgnc_id": 10660,
"hgvs_c": "c.1072C>A",
"hgvs_p": "p.Leu358Met",
"transcript": "ENST00000937355.1",
"protein_id": "ENSP00000607414.1",
"transcript_support_level": null,
"aa_start": 358,
"aa_end": null,
"aa_length": 426,
"cds_start": 1072,
"cds_end": null,
"cds_length": 1281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000937355.1"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDC3",
"gene_hgnc_id": 10660,
"hgvs_c": "c.1087C>A",
"hgvs_p": "p.Leu363Met",
"transcript": "XM_011542463.1",
"protein_id": "XP_011540765.1",
"transcript_support_level": null,
"aa_start": 363,
"aa_end": null,
"aa_length": 431,
"cds_start": 1087,
"cds_end": null,
"cds_length": 1296,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011542463.1"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDC3",
"gene_hgnc_id": 10660,
"hgvs_c": "c.1084C>A",
"hgvs_p": "p.Leu362Met",
"transcript": "XM_011542464.3",
"protein_id": "XP_011540766.1",
"transcript_support_level": null,
"aa_start": 362,
"aa_end": null,
"aa_length": 430,
"cds_start": 1084,
"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": "XM_011542464.3"
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDC3",
"gene_hgnc_id": 10660,
"hgvs_c": "c.994C>A",
"hgvs_p": "p.Leu332Met",
"transcript": "XM_011542466.2",
"protein_id": "XP_011540768.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 400,
"cds_start": 994,
"cds_end": null,
"cds_length": 1203,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011542466.2"
}
],
"gene_symbol": "SDC3",
"gene_hgnc_id": 10660,
"dbsnp": "rs904566879",
"frequency_reference_population": 0.000002053464,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205346,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3201870918273926,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.126,
"revel_prediction": "Benign",
"alphamissense_score": 0.2896,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.37,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.351,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_014654.4",
"gene_symbol": "SDC3",
"hgnc_id": 10660,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1120C>A",
"hgvs_p": "p.Leu374Met"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}