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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: 2-20202771-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=20202771&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 20202771,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_002997.5",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDC1",
"gene_hgnc_id": 10658,
"hgvs_c": "c.928G>T",
"hgvs_p": "p.Ala310Ser",
"transcript": "NM_002997.5",
"protein_id": "NP_002988.4",
"transcript_support_level": null,
"aa_start": 310,
"aa_end": null,
"aa_length": 310,
"cds_start": 928,
"cds_end": null,
"cds_length": 933,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000254351.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002997.5"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDC1",
"gene_hgnc_id": 10658,
"hgvs_c": "c.928G>T",
"hgvs_p": "p.Ala310Ser",
"transcript": "ENST00000254351.9",
"protein_id": "ENSP00000254351.4",
"transcript_support_level": 1,
"aa_start": 310,
"aa_end": null,
"aa_length": 310,
"cds_start": 928,
"cds_end": null,
"cds_length": 933,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002997.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000254351.9"
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SDC1",
"gene_hgnc_id": 10658,
"hgvs_c": "c.479-470G>T",
"hgvs_p": null,
"transcript": "ENST00000403076.5",
"protein_id": "ENSP00000384613.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 169,
"cds_start": null,
"cds_end": null,
"cds_length": 510,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000403076.5"
},
{
"aa_ref": "A",
"aa_alt": "S",
"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": "SDC1",
"gene_hgnc_id": 10658,
"hgvs_c": "c.928G>T",
"hgvs_p": "p.Ala310Ser",
"transcript": "NM_001006946.2",
"protein_id": "NP_001006947.2",
"transcript_support_level": null,
"aa_start": 310,
"aa_end": null,
"aa_length": 310,
"cds_start": 928,
"cds_end": null,
"cds_length": 933,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001006946.2"
},
{
"aa_ref": "A",
"aa_alt": "S",
"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": "SDC1",
"gene_hgnc_id": 10658,
"hgvs_c": "c.928G>T",
"hgvs_p": "p.Ala310Ser",
"transcript": "ENST00000381150.5",
"protein_id": "ENSP00000370542.1",
"transcript_support_level": 5,
"aa_start": 310,
"aa_end": null,
"aa_length": 310,
"cds_start": 928,
"cds_end": null,
"cds_length": 933,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000381150.5"
},
{
"aa_ref": "A",
"aa_alt": "S",
"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": "SDC1",
"gene_hgnc_id": 10658,
"hgvs_c": "c.922G>T",
"hgvs_p": "p.Ala308Ser",
"transcript": "ENST00000917369.1",
"protein_id": "ENSP00000587428.1",
"transcript_support_level": null,
"aa_start": 308,
"aa_end": null,
"aa_length": 308,
"cds_start": 922,
"cds_end": null,
"cds_length": 927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917369.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDC1",
"gene_hgnc_id": 10658,
"hgvs_c": "c.841G>T",
"hgvs_p": "p.Ala281Ser",
"transcript": "ENST00000852541.1",
"protein_id": "ENSP00000522600.1",
"transcript_support_level": null,
"aa_start": 281,
"aa_end": null,
"aa_length": 281,
"cds_start": 841,
"cds_end": null,
"cds_length": 846,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000852541.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDC1",
"gene_hgnc_id": 10658,
"hgvs_c": "c.835G>T",
"hgvs_p": "p.Ala279Ser",
"transcript": "ENST00000852542.1",
"protein_id": "ENSP00000522601.1",
"transcript_support_level": null,
"aa_start": 279,
"aa_end": null,
"aa_length": 279,
"cds_start": 835,
"cds_end": null,
"cds_length": 840,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000852542.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDC1",
"gene_hgnc_id": 10658,
"hgvs_c": "c.535G>T",
"hgvs_p": "p.Ala179Ser",
"transcript": "ENST00000970834.1",
"protein_id": "ENSP00000640893.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 179,
"cds_start": 535,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970834.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDC1",
"gene_hgnc_id": 10658,
"hgvs_c": "c.1000G>T",
"hgvs_p": "p.Ala334Ser",
"transcript": "XM_005262620.5",
"protein_id": "XP_005262677.1",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 334,
"cds_start": 1000,
"cds_end": null,
"cds_length": 1005,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005262620.5"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDC1",
"gene_hgnc_id": 10658,
"hgvs_c": "c.913G>T",
"hgvs_p": "p.Ala305Ser",
"transcript": "XM_005262621.3",
"protein_id": "XP_005262678.3",
"transcript_support_level": null,
"aa_start": 305,
"aa_end": null,
"aa_length": 305,
"cds_start": 913,
"cds_end": null,
"cds_length": 918,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005262621.3"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDC1",
"gene_hgnc_id": 10658,
"hgvs_c": "c.874G>T",
"hgvs_p": "p.Ala292Ser",
"transcript": "XM_005262622.3",
"protein_id": "XP_005262679.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 292,
"cds_start": 874,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005262622.3"
}
],
"gene_symbol": "SDC1",
"gene_hgnc_id": 10658,
"dbsnp": "rs774301421",
"frequency_reference_population": 6.8842263e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.88423e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8666694164276123,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.337,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.579,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.13,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.905,
"phylop100way_prediction": "Pathogenic",
"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": 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": "NM_002997.5",
"gene_symbol": "SDC1",
"hgnc_id": 10658,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.928G>T",
"hgvs_p": "p.Ala310Ser"
}
],
"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
}