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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: 7-129212401-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=129212401&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM2",
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SMO",
"hgnc_id": 11119,
"hgvs_c": "c.2314C>G",
"hgvs_p": "p.Arg772Gly",
"inheritance_mode": "AR,AD",
"pathogenic_score": 2,
"score": 1,
"transcript": "NM_005631.5",
"verdict": "Uncertain_significance"
},
{
"benign_score": 1,
"criteria": [
"PM2",
"BP4"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000243230",
"hgnc_id": null,
"hgvs_c": "n.129+1016G>C",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 1,
"transcript": "ENST00000466717.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_score": 1,
"allele_count_reference_population": 3,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.3068,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.08,
"chr": "7",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.4168831706047058,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 787,
"aa_ref": "R",
"aa_start": 772,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3977,
"cdna_start": 2833,
"cds_end": null,
"cds_length": 2364,
"cds_start": 2314,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_005631.5",
"gene_hgnc_id": 11119,
"gene_symbol": "SMO",
"hgvs_c": "c.2314C>G",
"hgvs_p": "p.Arg772Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000249373.8",
"protein_coding": true,
"protein_id": "NP_005622.1",
"strand": true,
"transcript": "NM_005631.5",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 787,
"aa_ref": "R",
"aa_start": 772,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3977,
"cdna_start": 2833,
"cds_end": null,
"cds_length": 2364,
"cds_start": 2314,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000249373.8",
"gene_hgnc_id": 11119,
"gene_symbol": "SMO",
"hgvs_c": "c.2314C>G",
"hgvs_p": "p.Arg772Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005631.5",
"protein_coding": true,
"protein_id": "ENSP00000249373.3",
"strand": true,
"transcript": "ENST00000249373.8",
"transcript_support_level": 1
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 786,
"aa_ref": "R",
"aa_start": 771,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4096,
"cdna_start": 2952,
"cds_end": null,
"cds_length": 2361,
"cds_start": 2311,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000925241.1",
"gene_hgnc_id": 11119,
"gene_symbol": "SMO",
"hgvs_c": "c.2311C>G",
"hgvs_p": "p.Arg771Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595300.1",
"strand": true,
"transcript": "ENST00000925241.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 784,
"aa_ref": "R",
"aa_start": 769,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3944,
"cdna_start": 2799,
"cds_end": null,
"cds_length": 2355,
"cds_start": 2305,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000925243.1",
"gene_hgnc_id": 11119,
"gene_symbol": "SMO",
"hgvs_c": "c.2305C>G",
"hgvs_p": "p.Arg769Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595302.1",
"strand": true,
"transcript": "ENST00000925243.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 476,
"aa_ref": "R",
"aa_start": 461,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2930,
"cdna_start": 1786,
"cds_end": null,
"cds_length": 1431,
"cds_start": 1381,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000925244.1",
"gene_hgnc_id": 11119,
"gene_symbol": "SMO",
"hgvs_c": "c.1381C>G",
"hgvs_p": "p.Arg461Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595303.1",
"strand": true,
"transcript": "ENST00000925244.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 450,
"aa_ref": "R",
"aa_start": 435,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2944,
"cdna_start": 1800,
"cds_end": null,
"cds_length": 1353,
"cds_start": 1303,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000925242.1",
"gene_hgnc_id": 11119,
"gene_symbol": "SMO",
"hgvs_c": "c.1303C>G",
"hgvs_p": "p.Arg435Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000595301.1",
"strand": true,
"transcript": "ENST00000925242.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 657,
"aa_ref": "R",
"aa_start": 642,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4091,
"cdna_start": 2947,
"cds_end": null,
"cds_length": 1974,
"cds_start": 1924,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "XM_047420759.1",
"gene_hgnc_id": 11119,
"gene_symbol": "SMO",
"hgvs_c": "c.1924C>G",
"hgvs_p": "p.Arg642Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047276715.1",
"strand": true,
"transcript": "XM_047420759.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3997,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000655644.1",
"gene_hgnc_id": 11119,
"gene_symbol": "SMO",
"hgvs_c": "n.*2069C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000499377.1",
"strand": true,
"transcript": "ENST00000655644.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3997,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000655644.1",
"gene_hgnc_id": 11119,
"gene_symbol": "SMO",
"hgvs_c": "n.*2069C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000499377.1",
"strand": true,
"transcript": "ENST00000655644.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 535,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000466717.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000243230",
"hgvs_c": "n.129+1016G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000466717.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 582,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000475779.1",
"gene_hgnc_id": 11119,
"gene_symbol": "SMO",
"hgvs_c": "n.*618C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000420749.1",
"strand": true,
"transcript": "ENST00000475779.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs140172891",
"effect": "missense_variant",
"frequency_reference_population": 0.0000018588305,
"gene_hgnc_id": 11119,
"gene_symbol": "SMO",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000136831,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.0000065678,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.47,
"pos": 129212401,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.586,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_005631.5"
}
]
}