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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: 6-158977577-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=158977577&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 158977577,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_001346418.1",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH3",
"gene_hgnc_id": 21054,
"hgvs_c": "c.1218A>G",
"hgvs_p": "p.Thr406Thr",
"transcript": "NM_031924.8",
"protein_id": "NP_114130.4",
"transcript_support_level": null,
"aa_start": 406,
"aa_end": null,
"aa_length": 418,
"cds_start": 1218,
"cds_end": null,
"cds_length": 1257,
"cdna_start": 1870,
"cdna_end": null,
"cdna_length": 6576,
"mane_select": "ENST00000367069.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_031924.8"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH3",
"gene_hgnc_id": 21054,
"hgvs_c": "c.1218A>G",
"hgvs_p": "p.Thr406Thr",
"transcript": "ENST00000367069.7",
"protein_id": "ENSP00000356036.1",
"transcript_support_level": 1,
"aa_start": 406,
"aa_end": null,
"aa_length": 418,
"cds_start": 1218,
"cds_end": null,
"cds_length": 1257,
"cdna_start": 1870,
"cdna_end": null,
"cdna_length": 6576,
"mane_select": "NM_031924.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000367069.7"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH3",
"gene_hgnc_id": 21054,
"hgvs_c": "c.1356A>G",
"hgvs_p": "p.Thr452Thr",
"transcript": "NM_001346418.1",
"protein_id": "NP_001333347.1",
"transcript_support_level": null,
"aa_start": 452,
"aa_end": null,
"aa_length": 464,
"cds_start": 1356,
"cds_end": null,
"cds_length": 1395,
"cdna_start": 1567,
"cdna_end": null,
"cdna_length": 6273,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001346418.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH3",
"gene_hgnc_id": 21054,
"hgvs_c": "c.1050A>G",
"hgvs_p": "p.Thr350Thr",
"transcript": "ENST00000884885.1",
"protein_id": "ENSP00000554944.1",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 362,
"cds_start": 1050,
"cds_end": null,
"cds_length": 1089,
"cdna_start": 1702,
"cdna_end": null,
"cdna_length": 2445,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884885.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH3",
"gene_hgnc_id": 21054,
"hgvs_c": "c.930A>G",
"hgvs_p": "p.Thr310Thr",
"transcript": "ENST00000449822.6",
"protein_id": "ENSP00000393195.1",
"transcript_support_level": 2,
"aa_start": 310,
"aa_end": null,
"aa_length": 322,
"cds_start": 930,
"cds_end": null,
"cds_length": 969,
"cdna_start": 1161,
"cdna_end": null,
"cdna_length": 8654,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000449822.6"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH3",
"gene_hgnc_id": 21054,
"hgvs_c": "c.828A>G",
"hgvs_p": "p.Thr276Thr",
"transcript": "XM_047419393.1",
"protein_id": "XP_047275349.1",
"transcript_support_level": null,
"aa_start": 276,
"aa_end": null,
"aa_length": 288,
"cds_start": 828,
"cds_end": null,
"cds_length": 867,
"cdna_start": 938,
"cdna_end": null,
"cdna_length": 5644,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047419393.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH3",
"gene_hgnc_id": 21054,
"hgvs_c": "n.1855A>G",
"hgvs_p": null,
"transcript": "NR_144434.1",
"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": 6227,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_144434.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH3",
"gene_hgnc_id": 21054,
"hgvs_c": "n.1870A>G",
"hgvs_p": null,
"transcript": "XR_001743668.3",
"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": 11578,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_001743668.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RSPH3",
"gene_hgnc_id": 21054,
"hgvs_c": "n.1582A>G",
"hgvs_p": null,
"transcript": "XR_001743670.3",
"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": 5954,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_001743670.3"
}
],
"gene_symbol": "RSPH3",
"gene_hgnc_id": 21054,
"dbsnp": "rs770469742",
"frequency_reference_population": 0.0000725067,
"hom_count_reference_population": 0,
"allele_count_reference_population": 117,
"gnomad_exomes_af": 0.0000739011,
"gnomad_genomes_af": 0.0000591203,
"gnomad_exomes_ac": 108,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9200000166893005,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.92,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.188,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Benign",
"transcript": "NM_001346418.1",
"gene_symbol": "RSPH3",
"hgnc_id": 21054,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1356A>G",
"hgvs_p": "p.Thr452Thr"
}
],
"clinvar_disease": "Primary ciliary dyskinesia 32",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Primary ciliary dyskinesia 32",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}