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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: 1-42930856-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=42930856&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 42930856,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000426263.10",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "c.286A>G",
"hgvs_p": "p.Met96Val",
"transcript": "NM_006516.4",
"protein_id": "NP_006507.2",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 492,
"cds_start": 286,
"cds_end": null,
"cds_length": 1479,
"cdna_start": 503,
"cdna_end": null,
"cdna_length": 3384,
"mane_select": "ENST00000426263.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "c.286A>G",
"hgvs_p": "p.Met96Val",
"transcript": "ENST00000426263.10",
"protein_id": "ENSP00000416293.2",
"transcript_support_level": 1,
"aa_start": 96,
"aa_end": null,
"aa_length": 492,
"cds_start": 286,
"cds_end": null,
"cds_length": 1479,
"cdna_start": 503,
"cdna_end": null,
"cdna_length": 3384,
"mane_select": "NM_006516.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "c.286A>G",
"hgvs_p": "p.Met96Val",
"transcript": "ENST00000674765.1",
"protein_id": "ENSP00000501811.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 359,
"cds_start": 286,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 494,
"cdna_end": null,
"cdna_length": 1851,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"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": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "c.184A>G",
"hgvs_p": "p.Met62Val",
"transcript": "ENST00000475162.3",
"protein_id": "ENSP00000487213.1",
"transcript_support_level": 5,
"aa_start": 62,
"aa_end": null,
"aa_length": 141,
"cds_start": 184,
"cds_end": null,
"cds_length": 426,
"cdna_start": 185,
"cdna_end": null,
"cdna_length": 598,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "c.190A>G",
"hgvs_p": "p.Met64Val",
"transcript": "ENST00000372500.4",
"protein_id": "ENSP00000361578.4",
"transcript_support_level": 3,
"aa_start": 64,
"aa_end": null,
"aa_length": 115,
"cds_start": 190,
"cds_end": null,
"cds_length": 348,
"cdna_start": 375,
"cdna_end": null,
"cdna_length": 533,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "n.494A>G",
"hgvs_p": null,
"transcript": "ENST00000625233.2",
"protein_id": null,
"transcript_support_level": 2,
"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": 1031,
"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": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "n.286A>G",
"hgvs_p": null,
"transcript": "ENST00000630287.2",
"protein_id": "ENSP00000486694.1",
"transcript_support_level": 5,
"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": 2398,
"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": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "n.309A>G",
"hgvs_p": null,
"transcript": "ENST00000675112.1",
"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": 2652,
"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": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "n.735A>G",
"hgvs_p": null,
"transcript": "ENST00000676254.1",
"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": 2795,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"hgvs_c": "n.*104A>G",
"hgvs_p": null,
"transcript": "ENST00000415851.6",
"protein_id": null,
"transcript_support_level": 2,
"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": 578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC2A1",
"gene_hgnc_id": 11005,
"dbsnp": "rs753161833",
"frequency_reference_population": 0.0000013805843,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000138058,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8668730854988098,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.822,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.3737,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.26,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.167,
"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": 17,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 17,
"benign_score": 0,
"pathogenic_score": 17,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000426263.10",
"gene_symbol": "SLC2A1",
"hgnc_id": 11005,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,Unknown",
"hgvs_c": "c.286A>G",
"hgvs_p": "p.Met96Val"
}
],
"clinvar_disease": " autosomal recessive,Encephalopathy due to GLUT1 deficiency,GLUT1 deficiency syndrome 1,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:3",
"phenotype_combined": "GLUT1 deficiency syndrome 1, autosomal recessive|not provided|Encephalopathy due to GLUT1 deficiency",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}