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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: 10-132749597-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=132749597&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 132749597,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_005539.5",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5A",
"gene_hgnc_id": 6076,
"hgvs_c": "c.813G>A",
"hgvs_p": "p.Ser271Ser",
"transcript": "NM_005539.5",
"protein_id": "NP_005530.3",
"transcript_support_level": null,
"aa_start": 271,
"aa_end": null,
"aa_length": 412,
"cds_start": 813,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 1123,
"cdna_end": null,
"cdna_length": 3000,
"mane_select": "ENST00000368594.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5A",
"gene_hgnc_id": 6076,
"hgvs_c": "c.813G>A",
"hgvs_p": "p.Ser271Ser",
"transcript": "ENST00000368594.8",
"protein_id": "ENSP00000357583.3",
"transcript_support_level": 1,
"aa_start": 271,
"aa_end": null,
"aa_length": 412,
"cds_start": 813,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 1123,
"cdna_end": null,
"cdna_length": 3000,
"mane_select": "NM_005539.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5A",
"gene_hgnc_id": 6076,
"hgvs_c": "c.813G>A",
"hgvs_p": "p.Ser271Ser",
"transcript": "ENST00000368593.7",
"protein_id": "ENSP00000357582.3",
"transcript_support_level": 1,
"aa_start": 271,
"aa_end": null,
"aa_length": 387,
"cds_start": 813,
"cds_end": null,
"cds_length": 1164,
"cdna_start": 1061,
"cdna_end": null,
"cdna_length": 1432,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5A",
"gene_hgnc_id": 6076,
"hgvs_c": "c.621G>A",
"hgvs_p": "p.Ser207Ser",
"transcript": "NM_001321042.2",
"protein_id": "NP_001307971.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 348,
"cds_start": 621,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 1184,
"cdna_end": null,
"cdna_length": 3061,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5A",
"gene_hgnc_id": 6076,
"hgvs_c": "c.639G>A",
"hgvs_p": "p.Ser213Ser",
"transcript": "XM_017016204.2",
"protein_id": "XP_016871693.1",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 354,
"cds_start": 639,
"cds_end": null,
"cds_length": 1065,
"cdna_start": 695,
"cdna_end": null,
"cdna_length": 2572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5A",
"gene_hgnc_id": 6076,
"hgvs_c": "c.813G>A",
"hgvs_p": "p.Ser271Ser",
"transcript": "XM_017016205.2",
"protein_id": "XP_016871694.1",
"transcript_support_level": null,
"aa_start": 271,
"aa_end": null,
"aa_length": 307,
"cds_start": 813,
"cds_end": null,
"cds_length": 924,
"cdna_start": 1123,
"cdna_end": null,
"cdna_length": 3717,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5A",
"gene_hgnc_id": 6076,
"hgvs_c": "n.275G>A",
"hgvs_p": null,
"transcript": "ENST00000498337.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 565,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5A",
"gene_hgnc_id": 6076,
"hgvs_c": "n.1123G>A",
"hgvs_p": null,
"transcript": "XR_001747104.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5A",
"gene_hgnc_id": 6076,
"hgvs_c": "n.1123G>A",
"hgvs_p": null,
"transcript": "XR_007061962.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1599,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5A",
"gene_hgnc_id": 6076,
"hgvs_c": "n.1123G>A",
"hgvs_p": null,
"transcript": "XR_007061963.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1647,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "INPP5A",
"gene_hgnc_id": 6076,
"hgvs_c": "n.1123G>A",
"hgvs_p": null,
"transcript": "XR_945735.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5814,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "INPP5A",
"gene_hgnc_id": 6076,
"hgvs_c": "c.646-16176G>A",
"hgvs_p": null,
"transcript": "ENST00000342652.6",
"protein_id": "ENSP00000340707.6",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 276,
"cds_start": -4,
"cds_end": null,
"cds_length": 831,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 832,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "INPP5A",
"gene_hgnc_id": 6076,
"dbsnp": "rs143990293",
"frequency_reference_population": 0.0021252509,
"hom_count_reference_population": 8,
"allele_count_reference_population": 3428,
"gnomad_exomes_af": 0.00215798,
"gnomad_genomes_af": 0.0018115,
"gnomad_exomes_ac": 3152,
"gnomad_genomes_ac": 276,
"gnomad_exomes_homalt": 8,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5799999833106995,
"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": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.449,
"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": -17,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS2",
"acmg_by_gene": [
{
"score": -17,
"benign_score": 17,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_005539.5",
"gene_symbol": "INPP5A",
"hgnc_id": 6076,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.813G>A",
"hgvs_p": "p.Ser271Ser"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}