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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: 1-217782175-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=217782175&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate"
],
"effects": [
"missense_variant",
"splice_region_variant"
],
"gene_symbol": "SPATA17",
"hgnc_id": 25184,
"hgvs_c": "c.725G>T",
"hgvs_p": "p.Gly242Val",
"inheritance_mode": "AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_138796.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "SPATA17-AS1",
"hgnc_id": 41086,
"hgvs_c": "n.284C>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 4,
"score": 4,
"transcript": "NR_125784.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_score": 4,
"allele_count_reference_population": 3,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.6039,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.09,
"chr": "1",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8735700845718384,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 361,
"aa_ref": "G",
"aa_start": 242,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5798,
"cdna_start": 760,
"cds_end": null,
"cds_length": 1086,
"cds_start": 725,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 11,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_138796.4",
"gene_hgnc_id": 25184,
"gene_symbol": "SPATA17",
"hgvs_c": "c.725G>T",
"hgvs_p": "p.Gly242Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000366933.5",
"protein_coding": true,
"protein_id": "NP_620151.1",
"strand": true,
"transcript": "NM_138796.4",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 361,
"aa_ref": "G",
"aa_start": 242,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5798,
"cdna_start": 760,
"cds_end": null,
"cds_length": 1086,
"cds_start": 725,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 11,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000366933.5",
"gene_hgnc_id": 25184,
"gene_symbol": "SPATA17",
"hgvs_c": "c.725G>T",
"hgvs_p": "p.Gly242Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_138796.4",
"protein_coding": true,
"protein_id": "ENSP00000355900.4",
"strand": true,
"transcript": "ENST00000366933.5",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 361,
"aa_ref": "G",
"aa_start": 242,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5942,
"cdna_start": 760,
"cds_end": null,
"cds_length": 1086,
"cds_start": 725,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 11,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001375655.1",
"gene_hgnc_id": 25184,
"gene_symbol": "SPATA17",
"hgvs_c": "c.725G>T",
"hgvs_p": "p.Gly242Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001362584.1",
"strand": true,
"transcript": "NM_001375655.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 361,
"aa_ref": "G",
"aa_start": 242,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1408,
"cdna_start": 745,
"cds_end": null,
"cds_length": 1086,
"cds_start": 725,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000905764.1",
"gene_hgnc_id": 25184,
"gene_symbol": "SPATA17",
"hgvs_c": "c.725G>T",
"hgvs_p": "p.Gly242Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000575823.1",
"strand": true,
"transcript": "ENST00000905764.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 344,
"aa_ref": "G",
"aa_start": 225,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1201,
"cdna_start": 709,
"cds_end": null,
"cds_length": 1035,
"cds_start": 674,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000937952.1",
"gene_hgnc_id": 25184,
"gene_symbol": "SPATA17",
"hgvs_c": "c.674G>T",
"hgvs_p": "p.Gly225Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000608011.1",
"strand": true,
"transcript": "ENST00000937952.1",
"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": 420,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000415765.1",
"gene_hgnc_id": 41086,
"gene_symbol": "SPATA17-AS1",
"hgvs_c": "n.284C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000415765.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 769,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000492747.2",
"gene_hgnc_id": 25184,
"gene_symbol": "SPATA17",
"hgvs_c": "n.571G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000492747.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 747,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000849067.1",
"gene_hgnc_id": 41086,
"gene_symbol": "SPATA17-AS1",
"hgvs_c": "n.253C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000849067.1",
"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": 585,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000849068.1",
"gene_hgnc_id": 41086,
"gene_symbol": "SPATA17-AS1",
"hgvs_c": "n.196C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000849068.1",
"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": 653,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000849069.1",
"gene_hgnc_id": 41086,
"gene_symbol": "SPATA17-AS1",
"hgvs_c": "n.262C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000849069.1",
"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": 408,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000849070.1",
"gene_hgnc_id": 41086,
"gene_symbol": "SPATA17-AS1",
"hgvs_c": "n.272C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000849070.1",
"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": 420,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NR_125784.1",
"gene_hgnc_id": 41086,
"gene_symbol": "SPATA17-AS1",
"hgvs_c": "n.284C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_125784.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.930167938790376,
"dbsnp": "rs757055443",
"effect": "missense_variant,splice_region_variant",
"frequency_reference_population": 0.0000018917443,
"gene_hgnc_id": 25184,
"gene_symbol": "SPATA17",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.973e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131808,
"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": "Pathogenic",
"phylop100way_score": 7.823,
"pos": 217782175,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.689,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.8199999928474426,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_138796.4"
}
]
}