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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: 5-55528158-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=55528158&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "PLPP1",
"hgnc_id": 9228,
"hgvs_c": "c.58+6414T>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_176895.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.87,
"chr": "5",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8700000047683716,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 284,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1542,
"cdna_start": null,
"cds_end": null,
"cds_length": 855,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_003711.4",
"gene_hgnc_id": 9228,
"gene_symbol": "PLPP1",
"hgvs_c": "c.58+6414T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000307259.9",
"protein_coding": true,
"protein_id": "NP_003702.2",
"strand": false,
"transcript": "NM_003711.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 284,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1542,
"cdna_start": null,
"cds_end": null,
"cds_length": 855,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000307259.9",
"gene_hgnc_id": 9228,
"gene_symbol": "PLPP1",
"hgvs_c": "c.58+6414T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003711.4",
"protein_coding": true,
"protein_id": "ENSP00000302229.8",
"strand": false,
"transcript": "ENST00000307259.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 285,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1550,
"cdna_start": null,
"cds_end": null,
"cds_length": 858,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000264775.9",
"gene_hgnc_id": 9228,
"gene_symbol": "PLPP1",
"hgvs_c": "c.58+6414T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000264775.5",
"strand": false,
"transcript": "ENST00000264775.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 302,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1599,
"cdna_start": null,
"cds_end": null,
"cds_length": 909,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000962877.1",
"gene_hgnc_id": 9228,
"gene_symbol": "PLPP1",
"hgvs_c": "c.58+6414T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632936.1",
"strand": false,
"transcript": "ENST00000962877.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 288,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1559,
"cdna_start": null,
"cds_end": null,
"cds_length": 867,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000962876.1",
"gene_hgnc_id": 9228,
"gene_symbol": "PLPP1",
"hgvs_c": "c.58+6414T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632935.1",
"strand": false,
"transcript": "ENST00000962876.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 285,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1545,
"cdna_start": null,
"cds_end": null,
"cds_length": 858,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_176895.3",
"gene_hgnc_id": 9228,
"gene_symbol": "PLPP1",
"hgvs_c": "c.58+6414T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_795714.1",
"strand": false,
"transcript": "NM_176895.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 283,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1459,
"cdna_start": null,
"cds_end": null,
"cds_length": 852,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000908451.1",
"gene_hgnc_id": 9228,
"gene_symbol": "PLPP1",
"hgvs_c": "c.58+6414T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000578510.1",
"strand": false,
"transcript": "ENST00000908451.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 283,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1610,
"cdna_start": null,
"cds_end": null,
"cds_length": 852,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000962875.1",
"gene_hgnc_id": 9228,
"gene_symbol": "PLPP1",
"hgvs_c": "c.58+6414T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632934.1",
"strand": false,
"transcript": "ENST00000962875.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 225,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1363,
"cdna_start": null,
"cds_end": null,
"cds_length": 678,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000962878.1",
"gene_hgnc_id": 9228,
"gene_symbol": "PLPP1",
"hgvs_c": "c.58+6414T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632937.1",
"strand": false,
"transcript": "ENST00000962878.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 172,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1206,
"cdna_start": null,
"cds_end": null,
"cds_length": 519,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000908450.1",
"gene_hgnc_id": 9228,
"gene_symbol": "PLPP1",
"hgvs_c": "c.58+6414T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000578509.1",
"strand": false,
"transcript": "ENST00000908450.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 171,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1200,
"cdna_start": null,
"cds_end": null,
"cds_length": 516,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000962879.1",
"gene_hgnc_id": 9228,
"gene_symbol": "PLPP1",
"hgvs_c": "c.58+6414T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632938.1",
"strand": false,
"transcript": "ENST00000962879.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 171,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1174,
"cdna_start": null,
"cds_end": null,
"cds_length": 516,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000962880.1",
"gene_hgnc_id": 9228,
"gene_symbol": "PLPP1",
"hgvs_c": "c.58+6414T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632939.1",
"strand": false,
"transcript": "ENST00000962880.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 221,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1390,
"cdna_start": null,
"cds_end": null,
"cds_length": 666,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_006714724.4",
"gene_hgnc_id": 9228,
"gene_symbol": "PLPP1",
"hgvs_c": "c.21+6414T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006714787.1",
"strand": false,
"transcript": "XM_006714724.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 971,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000509667.5",
"gene_hgnc_id": 9228,
"gene_symbol": "PLPP1",
"hgvs_c": "n.58+6414T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000425052.1",
"strand": false,
"transcript": "ENST00000509667.5",
"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": 677,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000515132.5",
"gene_hgnc_id": 9228,
"gene_symbol": "PLPP1",
"hgvs_c": "n.393+6414T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000515132.5",
"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": 1697,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_103485.2",
"gene_hgnc_id": 9228,
"gene_symbol": "PLPP1",
"hgvs_c": "n.393+6414T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_103485.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1995039",
"effect": "intron_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 9228,
"gene_symbol": "PLPP1",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"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": "Benign",
"phylop100way_score": 0.297,
"pos": 55528158,
"ref": "A",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_176895.3"
}
]
}