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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: 6-35506146-CG-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=35506146&ref=CG&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2"
],
"effects": [
"frameshift_variant"
],
"gene_symbol": "TULP1",
"hgnc_id": 12423,
"hgvs_c": "c.855delC",
"hgvs_p": "p.Val286fs",
"inheritance_mode": "AD,AR",
"pathogenic_score": 10,
"score": 10,
"transcript": "NM_003322.6",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LINC03135",
"hgnc_id": 58100,
"hgvs_c": "n.121+8425delG",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "ENST00000722033.1",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LOC124901309",
"hgnc_id": null,
"hgvs_c": "n.76-2075delG",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "XR_007059561.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2",
"acmg_score": 10,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "6",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 542,
"aa_ref": "P",
"aa_start": 285,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2120,
"cdna_start": 893,
"cds_end": null,
"cds_length": 1629,
"cds_start": 855,
"consequences": [
"frameshift_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_003322.6",
"gene_hgnc_id": 12423,
"gene_symbol": "TULP1",
"hgvs_c": "c.855delC",
"hgvs_p": "p.Val286fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000229771.11",
"protein_coding": true,
"protein_id": "NP_003313.3",
"strand": false,
"transcript": "NM_003322.6",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 542,
"aa_ref": "P",
"aa_start": 285,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2120,
"cdna_start": 893,
"cds_end": null,
"cds_length": 1629,
"cds_start": 855,
"consequences": [
"frameshift_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000229771.11",
"gene_hgnc_id": 12423,
"gene_symbol": "TULP1",
"hgvs_c": "c.855delC",
"hgvs_p": "p.Val286fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003322.6",
"protein_coding": true,
"protein_id": "ENSP00000229771.6",
"strand": false,
"transcript": "ENST00000229771.11",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 489,
"aa_ref": "P",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1941,
"cdna_start": 714,
"cds_end": null,
"cds_length": 1470,
"cds_start": 696,
"consequences": [
"frameshift_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000322263.8",
"gene_hgnc_id": 12423,
"gene_symbol": "TULP1",
"hgvs_c": "c.696delC",
"hgvs_p": "p.Val233fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000319414.4",
"strand": false,
"transcript": "ENST00000322263.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 540,
"aa_ref": "P",
"aa_start": 283,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2084,
"cdna_start": 860,
"cds_end": null,
"cds_length": 1623,
"cds_start": 849,
"consequences": [
"frameshift_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000614066.4",
"gene_hgnc_id": 12423,
"gene_symbol": "TULP1",
"hgvs_c": "c.849delC",
"hgvs_p": "p.Val284fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000477534.1",
"strand": false,
"transcript": "ENST00000614066.4",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 489,
"aa_ref": "P",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1961,
"cdna_start": 734,
"cds_end": null,
"cds_length": 1470,
"cds_start": 696,
"consequences": [
"frameshift_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001289395.2",
"gene_hgnc_id": 12423,
"gene_symbol": "TULP1",
"hgvs_c": "c.696delC",
"hgvs_p": "p.Val233fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001276324.1",
"strand": false,
"transcript": "NM_001289395.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 812,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000373892.4",
"gene_hgnc_id": 12423,
"gene_symbol": "TULP1",
"hgvs_c": "n.457delC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000373892.4",
"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": 644,
"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": "ENST00000722033.1",
"gene_hgnc_id": 58100,
"gene_symbol": "LINC03135",
"hgvs_c": "n.121+8425delG",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000722033.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 509,
"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": "ENST00000722034.1",
"gene_hgnc_id": 58100,
"gene_symbol": "LINC03135",
"hgvs_c": "n.125-4226delG",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000722034.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 473,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000722035.1",
"gene_hgnc_id": 58100,
"gene_symbol": "LINC03135",
"hgvs_c": "n.204-2075delG",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000722035.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 505,
"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": "ENST00000722036.1",
"gene_hgnc_id": 58100,
"gene_symbol": "LINC03135",
"hgvs_c": "n.117-1683delG",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000722036.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 471,
"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": "ENST00000722037.1",
"gene_hgnc_id": 58100,
"gene_symbol": "LINC03135",
"hgvs_c": "n.207+1309delG",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000722037.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 855,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000722038.1",
"gene_hgnc_id": 58100,
"gene_symbol": "LINC03135",
"hgvs_c": "n.587-2075delG",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000722038.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 343,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_007059561.1",
"gene_hgnc_id": null,
"gene_symbol": "LOC124901309",
"hgvs_c": "n.76-2075delG",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_007059561.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 513,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000496434.5",
"gene_hgnc_id": 12423,
"gene_symbol": "TULP1",
"hgvs_c": "n.-129delC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000496434.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1554125752",
"effect": "frameshift_variant",
"frequency_reference_population": 6.8436435e-7,
"gene_hgnc_id": 12423,
"gene_symbol": "TULP1",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84364e-7,
"gnomad_exomes_homalt": 0,
"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": -1.082,
"pos": 35506146,
"ref": "CG",
"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_003322.6"
}
]
}