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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: 7-75496693-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=75496693&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SPDYE5",
"hgnc_id": 35464,
"hgvs_c": "c.399C>G",
"hgvs_p": "p.Ser133Arg",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_001306141.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "PMS2P3",
"hgnc_id": null,
"hgvs_c": "n.435-5070G>C",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000845725.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.2867,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.48,
"chr": "7",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.07762956619262695,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 402,
"aa_ref": "S",
"aa_start": 133,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3281,
"cdna_start": 942,
"cds_end": null,
"cds_length": 1209,
"cds_start": 399,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001306141.4",
"gene_hgnc_id": 35464,
"gene_symbol": "SPDYE5",
"hgvs_c": "c.399C>G",
"hgvs_p": "p.Ser133Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000625065.4",
"protein_coding": true,
"protein_id": "NP_001293070.1",
"strand": true,
"transcript": "NM_001306141.4",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 402,
"aa_ref": "S",
"aa_start": 133,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3281,
"cdna_start": 942,
"cds_end": null,
"cds_length": 1209,
"cds_start": 399,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000625065.4",
"gene_hgnc_id": 35464,
"gene_symbol": "SPDYE5",
"hgvs_c": "c.399C>G",
"hgvs_p": "p.Ser133Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001306141.4",
"protein_coding": true,
"protein_id": "ENSP00000485398.1",
"strand": true,
"transcript": "ENST00000625065.4",
"transcript_support_level": 5
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 402,
"aa_ref": "S",
"aa_start": 133,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3873,
"cdna_start": 2817,
"cds_end": null,
"cds_length": 1209,
"cds_start": 399,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047420408.1",
"gene_hgnc_id": 35464,
"gene_symbol": "SPDYE5",
"hgvs_c": "c.399C>G",
"hgvs_p": "p.Ser133Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047276364.1",
"strand": true,
"transcript": "XM_047420408.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 227,
"aa_ref": "S",
"aa_start": 133,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3165,
"cdna_start": 2810,
"cds_end": null,
"cds_length": 684,
"cds_start": 399,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047420407.1",
"gene_hgnc_id": 35464,
"gene_symbol": "SPDYE5",
"hgvs_c": "c.399C>G",
"hgvs_p": "p.Ser133Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047276363.1",
"strand": true,
"transcript": "XM_047420407.1",
"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": 1645,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000845725.1",
"gene_hgnc_id": null,
"gene_symbol": "PMS2P3",
"hgvs_c": "n.435-5070G>C",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000845725.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs782677248",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 35464,
"gene_symbol": "SPDYE5",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.91904e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"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": -0.872,
"pos": 75496693,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001306141.4"
}
]
}