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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: 6-47973528-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=47973528&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 47973528,
"ref": "A",
"alt": "C",
"effect": "intron_variant",
"transcript": "ENST00000339488.9",
"consequences": [
{
"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": 4,
"intron_rank_end": null,
"gene_symbol": "PTCHD4",
"gene_hgnc_id": 21345,
"hgvs_c": "c.898+35106T>G",
"hgvs_p": null,
"transcript": "NM_001384253.1",
"protein_id": "NP_001371182.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 843,
"cds_start": -4,
"cds_end": null,
"cds_length": 2532,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 25280,
"mane_select": "ENST00000339488.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PTCHD4",
"gene_hgnc_id": 21345,
"hgvs_c": "c.898+35106T>G",
"hgvs_p": null,
"transcript": "ENST00000339488.9",
"protein_id": "ENSP00000341914.5",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 843,
"cds_start": -4,
"cds_end": null,
"cds_length": 2532,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 25280,
"mane_select": "NM_001384253.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank_end": null,
"gene_symbol": "PTCHD4",
"gene_hgnc_id": 21345,
"hgvs_c": "c.898+35106T>G",
"hgvs_p": null,
"transcript": "ENST00000398738.3",
"protein_id": "ENSP00000381722.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 308,
"cds_start": -4,
"cds_end": null,
"cds_length": 927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4671,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PTCHD4",
"gene_hgnc_id": 21345,
"hgvs_c": "c.907+35106T>G",
"hgvs_p": null,
"transcript": "NM_001013732.4",
"protein_id": "NP_001013754.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 846,
"cds_start": -4,
"cds_end": null,
"cds_length": 2541,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 24346,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank_end": null,
"gene_symbol": "PTCHD4",
"gene_hgnc_id": 21345,
"hgvs_c": "c.1072+35106T>G",
"hgvs_p": null,
"transcript": "ENST00000679966.1",
"protein_id": "ENSP00000506133.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 366,
"cds_start": -4,
"cds_end": null,
"cds_length": 1101,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4845,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PTCHD4",
"gene_hgnc_id": 21345,
"hgvs_c": "c.907+35106T>G",
"hgvs_p": null,
"transcript": "NM_207499.2",
"protein_id": "NP_997382.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 311,
"cds_start": -4,
"cds_end": null,
"cds_length": 936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3268,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank_end": null,
"gene_symbol": "PTCHD4",
"gene_hgnc_id": 21345,
"hgvs_c": "c.898+35106T>G",
"hgvs_p": null,
"transcript": "NM_001410910.1",
"protein_id": "NP_001397839.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 308,
"cds_start": -4,
"cds_end": null,
"cds_length": 927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4342,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PTCHD4",
"gene_hgnc_id": 21345,
"hgvs_c": "c.1081+35106T>G",
"hgvs_p": null,
"transcript": "XM_017010891.2",
"protein_id": "XP_016866380.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 904,
"cds_start": -4,
"cds_end": null,
"cds_length": 2715,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 24345,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PTCHD4",
"gene_hgnc_id": 21345,
"hgvs_c": "c.1072+35106T>G",
"hgvs_p": null,
"transcript": "XM_017010892.2",
"protein_id": "XP_016866381.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 901,
"cds_start": -4,
"cds_end": null,
"cds_length": 2706,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 24509,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PTCHD4",
"gene_hgnc_id": 21345,
"hgvs_c": "c.661+35106T>G",
"hgvs_p": null,
"transcript": "XM_047418830.1",
"protein_id": "XP_047274786.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 764,
"cds_start": -4,
"cds_end": null,
"cds_length": 2295,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 23953,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PTCHD4",
"gene_hgnc_id": 21345,
"hgvs_c": "c.148+35106T>G",
"hgvs_p": null,
"transcript": "XM_011514639.3",
"protein_id": "XP_011512941.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 593,
"cds_start": -4,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 23894,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PTCHD4",
"gene_hgnc_id": 21345,
"hgvs_c": "c.97+35057T>G",
"hgvs_p": null,
"transcript": "XM_017010895.2",
"protein_id": "XP_016866384.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 576,
"cds_start": -4,
"cds_end": null,
"cds_length": 1731,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 23455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTCHD4",
"gene_hgnc_id": 21345,
"dbsnp": "rs2814478",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9300000071525574,
"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": -0.93,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.403,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000339488.9",
"gene_symbol": "PTCHD4",
"hgnc_id": 21345,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.898+35106T>G",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}