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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: X-15331839-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=15331839&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 15331839,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001440789.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.92G>A",
"hgvs_p": "p.Arg31His",
"transcript": "NM_002641.4",
"protein_id": "NP_002632.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 484,
"cds_start": 92,
"cds_end": null,
"cds_length": 1455,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000333590.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002641.4"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.92G>A",
"hgvs_p": "p.Arg31His",
"transcript": "ENST00000333590.6",
"protein_id": "ENSP00000369820.3",
"transcript_support_level": 1,
"aa_start": 31,
"aa_end": null,
"aa_length": 484,
"cds_start": 92,
"cds_end": null,
"cds_length": 1455,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002641.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000333590.6"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.92G>A",
"hgvs_p": "p.Arg31His",
"transcript": "NM_001440789.1",
"protein_id": "NP_001427718.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 515,
"cds_start": 92,
"cds_end": null,
"cds_length": 1548,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440789.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.92G>A",
"hgvs_p": "p.Arg31His",
"transcript": "ENST00000542278.6",
"protein_id": "ENSP00000442653.2",
"transcript_support_level": 5,
"aa_start": 31,
"aa_end": null,
"aa_length": 484,
"cds_start": 92,
"cds_end": null,
"cds_length": 1455,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000542278.6"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.92G>A",
"hgvs_p": "p.Arg31His",
"transcript": "ENST00000482148.6",
"protein_id": "ENSP00000489528.1",
"transcript_support_level": 5,
"aa_start": 31,
"aa_end": null,
"aa_length": 315,
"cds_start": 92,
"cds_end": null,
"cds_length": 948,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000482148.6"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.92G>A",
"hgvs_p": "p.Arg31His",
"transcript": "ENST00000635543.1",
"protein_id": "ENSP00000489205.1",
"transcript_support_level": 4,
"aa_start": 31,
"aa_end": null,
"aa_length": 151,
"cds_start": 92,
"cds_end": null,
"cds_length": 457,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000635543.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.14-3526G>A",
"hgvs_p": null,
"transcript": "NM_001440790.1",
"protein_id": "NP_001427719.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 281,
"cds_start": null,
"cds_end": null,
"cds_length": 846,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440790.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.13+3662G>A",
"hgvs_p": null,
"transcript": "NM_020473.3",
"protein_id": "NP_065206.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 250,
"cds_start": null,
"cds_end": null,
"cds_length": 753,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020473.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.13+3662G>A",
"hgvs_p": null,
"transcript": "ENST00000634582.1",
"protein_id": "ENSP00000489540.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 250,
"cds_start": null,
"cds_end": null,
"cds_length": 753,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000634582.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.-315+35G>A",
"hgvs_p": null,
"transcript": "ENST00000637296.1",
"protein_id": "ENSP00000490545.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 169,
"cds_start": null,
"cds_end": null,
"cds_length": 510,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000637296.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "c.-231+35G>A",
"hgvs_p": null,
"transcript": "ENST00000634640.1",
"protein_id": "ENSP00000489083.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 149,
"cds_start": null,
"cds_end": null,
"cds_length": 451,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000634640.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.177G>A",
"hgvs_p": null,
"transcript": "ENST00000635045.1",
"protein_id": null,
"transcript_support_level": 2,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000635045.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.92G>A",
"hgvs_p": null,
"transcript": "ENST00000635598.1",
"protein_id": "ENSP00000489207.1",
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000635598.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.92G>A",
"hgvs_p": null,
"transcript": "ENST00000637626.1",
"protein_id": "ENSP00000489928.1",
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000637626.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.92G>A",
"hgvs_p": null,
"transcript": "ENST00000638131.1",
"protein_id": "ENSP00000490483.1",
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000638131.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.208G>A",
"hgvs_p": null,
"transcript": "NR_033835.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_033835.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.177G>A",
"hgvs_p": null,
"transcript": "NR_199789.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_199789.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.142+35G>A",
"hgvs_p": null,
"transcript": "ENST00000474662.2",
"protein_id": null,
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000474662.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.173+35G>A",
"hgvs_p": null,
"transcript": "NR_033836.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_033836.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.142+35G>A",
"hgvs_p": null,
"transcript": "NR_199790.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_199790.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"hgvs_c": "n.-116G>A",
"hgvs_p": null,
"transcript": "ENST00000634286.1",
"protein_id": "ENSP00000489491.1",
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000634286.1"
}
],
"gene_symbol": "PIGA",
"gene_hgnc_id": 8957,
"dbsnp": "rs758863767",
"frequency_reference_population": 0.000022311873,
"hom_count_reference_population": 7,
"allele_count_reference_population": 27,
"gnomad_exomes_af": 0.0000218562,
"gnomad_genomes_af": 0.0000267778,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.04939335584640503,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.062,
"revel_prediction": "Benign",
"alphamissense_score": 0.0734,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.92,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.462,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "PM1,BP4_Strong,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 16,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001440789.1",
"gene_symbol": "PIGA",
"hgnc_id": 8957,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,XL,AD",
"hgvs_c": "c.92G>A",
"hgvs_p": "p.Arg31His"
}
],
"clinvar_disease": "Inborn genetic diseases,Multiple congenital anomalies-hypotonia-seizures syndrome 2",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "Multiple congenital anomalies-hypotonia-seizures syndrome 2|Inborn genetic diseases",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}