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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: 10-132749566-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=132749566&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 132749566,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_005539.5",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.782A>G",
"hgvs_p": "p.Asn261Ser",
"transcript": "NM_005539.5",
"protein_id": "NP_005530.3",
"transcript_support_level": null,
"aa_start": 261,
"aa_end": null,
"aa_length": 412,
"cds_start": 782,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 1092,
"cdna_end": null,
"cdna_length": 3000,
"mane_select": "ENST00000368594.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.782A>G",
"hgvs_p": "p.Asn261Ser",
"transcript": "ENST00000368594.8",
"protein_id": "ENSP00000357583.3",
"transcript_support_level": 1,
"aa_start": 261,
"aa_end": null,
"aa_length": 412,
"cds_start": 782,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 1092,
"cdna_end": null,
"cdna_length": 3000,
"mane_select": "NM_005539.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.782A>G",
"hgvs_p": "p.Asn261Ser",
"transcript": "ENST00000368593.7",
"protein_id": "ENSP00000357582.3",
"transcript_support_level": 1,
"aa_start": 261,
"aa_end": null,
"aa_length": 387,
"cds_start": 782,
"cds_end": null,
"cds_length": 1164,
"cdna_start": 1030,
"cdna_end": null,
"cdna_length": 1432,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.590A>G",
"hgvs_p": "p.Asn197Ser",
"transcript": "NM_001321042.2",
"protein_id": "NP_001307971.1",
"transcript_support_level": null,
"aa_start": 197,
"aa_end": null,
"aa_length": 348,
"cds_start": 590,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 1153,
"cdna_end": null,
"cdna_length": 3061,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.608A>G",
"hgvs_p": "p.Asn203Ser",
"transcript": "XM_017016204.2",
"protein_id": "XP_016871693.1",
"transcript_support_level": null,
"aa_start": 203,
"aa_end": null,
"aa_length": 354,
"cds_start": 608,
"cds_end": null,
"cds_length": 1065,
"cdna_start": 664,
"cdna_end": null,
"cdna_length": 2572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_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.782A>G",
"hgvs_p": "p.Asn261Ser",
"transcript": "XM_017016205.2",
"protein_id": "XP_016871694.1",
"transcript_support_level": null,
"aa_start": 261,
"aa_end": null,
"aa_length": 307,
"cds_start": 782,
"cds_end": null,
"cds_length": 924,
"cdna_start": 1092,
"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.244A>G",
"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.1092A>G",
"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.1092A>G",
"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.1092A>G",
"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.1092A>G",
"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.646-16207A>G",
"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": "rs781476790",
"frequency_reference_population": 0.00002294036,
"hom_count_reference_population": 1,
"allele_count_reference_population": 37,
"gnomad_exomes_af": 0.0000225923,
"gnomad_genomes_af": 0.0000262805,
"gnomad_exomes_ac": 33,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2666814923286438,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.119,
"revel_prediction": "Benign",
"alphamissense_score": 0.0711,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.55,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.142,
"phylop100way_prediction": "Pathogenic",
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "NM_005539.5",
"gene_symbol": "INPP5A",
"hgnc_id": 6076,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.782A>G",
"hgvs_p": "p.Asn261Ser"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}