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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: 2-130340975-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=130340975&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 130340975,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_032357.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "E",
"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": "VMA22",
"gene_hgnc_id": 28178,
"hgvs_c": "c.363C>A",
"hgvs_p": "p.Asp121Glu",
"transcript": "NM_032357.4",
"protein_id": "NP_115733.2",
"transcript_support_level": null,
"aa_start": 121,
"aa_end": null,
"aa_length": 180,
"cds_start": 363,
"cds_end": null,
"cds_length": 543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000259229.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032357.4"
},
{
"aa_ref": "D",
"aa_alt": "E",
"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": "VMA22",
"gene_hgnc_id": 28178,
"hgvs_c": "c.363C>A",
"hgvs_p": "p.Asp121Glu",
"transcript": "ENST00000259229.7",
"protein_id": "ENSP00000259229.2",
"transcript_support_level": 1,
"aa_start": 121,
"aa_end": null,
"aa_length": 180,
"cds_start": 363,
"cds_end": null,
"cds_length": 543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_032357.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000259229.7"
},
{
"aa_ref": "D",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VMA22",
"gene_hgnc_id": 28178,
"hgvs_c": "c.363C>A",
"hgvs_p": "p.Asp121Glu",
"transcript": "ENST00000902736.1",
"protein_id": "ENSP00000572795.1",
"transcript_support_level": null,
"aa_start": 121,
"aa_end": null,
"aa_length": 222,
"cds_start": 363,
"cds_end": null,
"cds_length": 669,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902736.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"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": "VMA22",
"gene_hgnc_id": 28178,
"hgvs_c": "c.348C>A",
"hgvs_p": "p.Asp116Glu",
"transcript": "NM_001321118.1",
"protein_id": "NP_001308047.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 175,
"cds_start": 348,
"cds_end": null,
"cds_length": 528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321118.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"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": "VMA22",
"gene_hgnc_id": 28178,
"hgvs_c": "c.348C>A",
"hgvs_p": "p.Asp116Glu",
"transcript": "ENST00000409127.1",
"protein_id": "ENSP00000387301.1",
"transcript_support_level": 2,
"aa_start": 116,
"aa_end": null,
"aa_length": 175,
"cds_start": 348,
"cds_end": null,
"cds_length": 528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409127.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"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": "VMA22",
"gene_hgnc_id": 28178,
"hgvs_c": "c.339C>A",
"hgvs_p": "p.Asp113Glu",
"transcript": "NM_001321119.2",
"protein_id": "NP_001308048.2",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 172,
"cds_start": 339,
"cds_end": null,
"cds_length": 519,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321119.2"
},
{
"aa_ref": "D",
"aa_alt": "E",
"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": "VMA22",
"gene_hgnc_id": 28178,
"hgvs_c": "c.339C>A",
"hgvs_p": "p.Asp113Glu",
"transcript": "ENST00000902734.1",
"protein_id": "ENSP00000572793.1",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 172,
"cds_start": 339,
"cds_end": null,
"cds_length": 519,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902734.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"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": "VMA22",
"gene_hgnc_id": 28178,
"hgvs_c": "c.291C>A",
"hgvs_p": "p.Asp97Glu",
"transcript": "ENST00000902735.1",
"protein_id": "ENSP00000572794.1",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 156,
"cds_start": 291,
"cds_end": null,
"cds_length": 471,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902735.1"
},
{
"aa_ref": "D",
"aa_alt": "E",
"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": "VMA22",
"gene_hgnc_id": 28178,
"hgvs_c": "c.219C>A",
"hgvs_p": "p.Asp73Glu",
"transcript": "ENST00000912734.1",
"protein_id": "ENSP00000582793.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 132,
"cds_start": 219,
"cds_end": null,
"cds_length": 399,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912734.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VMA22",
"gene_hgnc_id": 28178,
"hgvs_c": "n.363C>A",
"hgvs_p": null,
"transcript": "ENST00000442217.5",
"protein_id": "ENSP00000403480.1",
"transcript_support_level": 2,
"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": "ENST00000442217.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "VMA22",
"gene_hgnc_id": 28178,
"hgvs_c": "n.1161C>A",
"hgvs_p": null,
"transcript": "ENST00000465315.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000465315.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VMA22",
"gene_hgnc_id": 28178,
"hgvs_c": "n.348C>A",
"hgvs_p": null,
"transcript": "ENST00000651709.1",
"protein_id": "ENSP00000499101.1",
"transcript_support_level": null,
"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": "ENST00000651709.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VMA22",
"gene_hgnc_id": 28178,
"hgvs_c": "n.800C>A",
"hgvs_p": null,
"transcript": "NR_104471.1",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_104471.1"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VMA22",
"gene_hgnc_id": 28178,
"hgvs_c": "n.402C>A",
"hgvs_p": null,
"transcript": "NR_135548.2",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_135548.2"
}
],
"gene_symbol": "VMA22",
"gene_hgnc_id": 28178,
"dbsnp": "rs771683316",
"frequency_reference_population": 6.842604e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.8426e-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": 0.44983047246932983,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.459,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5976,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.46,
"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": 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_032357.4",
"gene_symbol": "VMA22",
"hgnc_id": 28178,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.363C>A",
"hgvs_p": "p.Asp121Glu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}