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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: 3-196707860-G-GT (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=196707860&ref=G&alt=GT&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5"
],
"effects": [
"frameshift_variant",
"stop_gained"
],
"gene_symbol": "CEP19",
"hgnc_id": 28209,
"hgvs_c": "c.182dupA",
"hgvs_p": "p.Tyr61fs",
"inheritance_mode": "AR",
"pathogenic_score": 7,
"score": 7,
"transcript": "NM_032898.5",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP5"
],
"effects": [
"intron_variant"
],
"gene_symbol": "PIGX",
"hgnc_id": 26046,
"hgvs_c": "c.-11-8997dupT",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 3,
"score": 3,
"transcript": "ENST00000426755.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5",
"acmg_score": 7,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "GT",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "3",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Bardet-Biedl syndrome",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": "*?",
"aa_end": null,
"aa_length": 163,
"aa_ref": "Y",
"aa_start": 61,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2158,
"cdna_start": 574,
"cds_end": null,
"cds_length": 492,
"cds_start": 182,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_032898.5",
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"hgvs_c": "c.182dupA",
"hgvs_p": "p.Tyr61fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000409690.5",
"protein_coding": true,
"protein_id": "NP_116287.3",
"strand": false,
"transcript": "NM_032898.5",
"transcript_support_level": null
},
{
"aa_alt": "*?",
"aa_end": null,
"aa_length": 163,
"aa_ref": "Y",
"aa_start": 61,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2158,
"cdna_start": 574,
"cds_end": null,
"cds_length": 492,
"cds_start": 182,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000409690.5",
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"hgvs_c": "c.182dupA",
"hgvs_p": "p.Tyr61fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_032898.5",
"protein_coding": true,
"protein_id": "ENSP00000387209.4",
"strand": false,
"transcript": "ENST00000409690.5",
"transcript_support_level": 1
},
{
"aa_alt": "*?",
"aa_end": null,
"aa_length": 163,
"aa_ref": "Y",
"aa_start": 61,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2155,
"cdna_start": 571,
"cds_end": null,
"cds_length": 492,
"cds_start": 182,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001379469.1",
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"hgvs_c": "c.182dupA",
"hgvs_p": "p.Tyr61fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001366398.1",
"strand": false,
"transcript": "NM_001379469.1",
"transcript_support_level": null
},
{
"aa_alt": "*?",
"aa_end": null,
"aa_length": 163,
"aa_ref": "Y",
"aa_start": 61,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1897,
"cdna_start": 313,
"cds_end": null,
"cds_length": 492,
"cds_start": 182,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001379470.1",
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"hgvs_c": "c.182dupA",
"hgvs_p": "p.Tyr61fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001366399.1",
"strand": false,
"transcript": "NM_001379470.1",
"transcript_support_level": null
},
{
"aa_alt": "*?",
"aa_end": null,
"aa_length": 163,
"aa_ref": "Y",
"aa_start": 61,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2208,
"cdna_start": 624,
"cds_end": null,
"cds_length": 492,
"cds_start": 182,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000893283.1",
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"hgvs_c": "c.182dupA",
"hgvs_p": "p.Tyr61fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000563342.1",
"strand": false,
"transcript": "ENST00000893283.1",
"transcript_support_level": null
},
{
"aa_alt": "*?",
"aa_end": null,
"aa_length": 163,
"aa_ref": "Y",
"aa_start": 61,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1168,
"cdna_start": 357,
"cds_end": null,
"cds_length": 492,
"cds_start": 182,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000893284.1",
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"hgvs_c": "c.182dupA",
"hgvs_p": "p.Tyr61fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000563343.1",
"strand": false,
"transcript": "ENST00000893284.1",
"transcript_support_level": null
},
{
"aa_alt": "*?",
"aa_end": null,
"aa_length": 163,
"aa_ref": "Y",
"aa_start": 61,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1383,
"cdna_start": 313,
"cds_end": null,
"cds_length": 492,
"cds_start": 182,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000893285.1",
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"hgvs_c": "c.182dupA",
"hgvs_p": "p.Tyr61fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000563344.1",
"strand": false,
"transcript": "ENST00000893285.1",
"transcript_support_level": null
},
{
"aa_alt": "*?",
"aa_end": null,
"aa_length": 163,
"aa_ref": "Y",
"aa_start": 61,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1124,
"cdna_start": 313,
"cds_end": null,
"cds_length": 492,
"cds_start": 182,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000893286.1",
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"hgvs_c": "c.182dupA",
"hgvs_p": "p.Tyr61fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000563345.1",
"strand": false,
"transcript": "ENST00000893286.1",
"transcript_support_level": null
},
{
"aa_alt": "*?",
"aa_end": null,
"aa_length": 163,
"aa_ref": "Y",
"aa_start": 61,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1909,
"cdna_start": 327,
"cds_end": null,
"cds_length": 492,
"cds_start": 182,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000933600.1",
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"hgvs_c": "c.182dupA",
"hgvs_p": "p.Tyr61fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603659.1",
"strand": false,
"transcript": "ENST00000933600.1",
"transcript_support_level": null
},
{
"aa_alt": "*?",
"aa_end": null,
"aa_length": 163,
"aa_ref": "Y",
"aa_start": 61,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1506,
"cdna_start": 675,
"cds_end": null,
"cds_length": 492,
"cds_start": 182,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000933601.1",
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"hgvs_c": "c.182dupA",
"hgvs_p": "p.Tyr61fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603660.1",
"strand": false,
"transcript": "ENST00000933601.1",
"transcript_support_level": null
},
{
"aa_alt": "*?",
"aa_end": null,
"aa_length": 163,
"aa_ref": "Y",
"aa_start": 61,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1935,
"cdna_start": 353,
"cds_end": null,
"cds_length": 492,
"cds_start": 182,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000959538.1",
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"hgvs_c": "c.182dupA",
"hgvs_p": "p.Tyr61fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629597.1",
"strand": false,
"transcript": "ENST00000959538.1",
"transcript_support_level": null
},
{
"aa_alt": "*?",
"aa_end": null,
"aa_length": 163,
"aa_ref": "Y",
"aa_start": 61,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2785,
"cdna_start": 1211,
"cds_end": null,
"cds_length": 492,
"cds_start": 182,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000959539.1",
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"hgvs_c": "c.182dupA",
"hgvs_p": "p.Tyr61fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629598.1",
"strand": false,
"transcript": "ENST00000959539.1",
"transcript_support_level": null
},
{
"aa_alt": "*?",
"aa_end": null,
"aa_length": 163,
"aa_ref": "Y",
"aa_start": 61,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2339,
"cdna_start": 746,
"cds_end": null,
"cds_length": 492,
"cds_start": 182,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000959540.1",
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"hgvs_c": "c.182dupA",
"hgvs_p": "p.Tyr61fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629599.1",
"strand": false,
"transcript": "ENST00000959540.1",
"transcript_support_level": null
},
{
"aa_alt": "*?",
"aa_end": null,
"aa_length": 163,
"aa_ref": "Y",
"aa_start": 61,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1859,
"cdna_start": 1048,
"cds_end": null,
"cds_length": 492,
"cds_start": 182,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000959541.1",
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"hgvs_c": "c.182dupA",
"hgvs_p": "p.Tyr61fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629600.1",
"strand": false,
"transcript": "ENST00000959541.1",
"transcript_support_level": null
},
{
"aa_alt": "*?",
"aa_end": null,
"aa_length": 163,
"aa_ref": "Y",
"aa_start": 61,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2392,
"cdna_start": 818,
"cds_end": null,
"cds_length": 492,
"cds_start": 182,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000959542.1",
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"hgvs_c": "c.182dupA",
"hgvs_p": "p.Tyr61fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629601.1",
"strand": false,
"transcript": "ENST00000959542.1",
"transcript_support_level": null
},
{
"aa_alt": "*?",
"aa_end": null,
"aa_length": 128,
"aa_ref": "Y",
"aa_start": 26,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1958,
"cdna_start": 374,
"cds_end": null,
"cds_length": 387,
"cds_start": 77,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001379468.1",
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"hgvs_c": "c.77dupA",
"hgvs_p": "p.Tyr26fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001366397.1",
"strand": false,
"transcript": "NM_001379468.1",
"transcript_support_level": null
},
{
"aa_alt": "*?",
"aa_end": null,
"aa_length": 128,
"aa_ref": "Y",
"aa_start": 26,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1172,
"cdna_start": 372,
"cds_end": null,
"cds_length": 387,
"cds_start": 77,
"consequences": [
"frameshift_variant",
"stop_gained"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000399942.4",
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"hgvs_c": "c.77dupA",
"hgvs_p": "p.Tyr26fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000382823.4",
"strand": false,
"transcript": "ENST00000399942.4",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 169,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 744,
"cdna_start": null,
"cds_end": null,
"cds_length": 511,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000426755.5",
"gene_hgnc_id": 26046,
"gene_symbol": "PIGX",
"hgvs_c": "c.-11-8997dupT",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000409073.1",
"strand": true,
"transcript": "ENST00000426755.5",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1553794304",
"effect": "frameshift_variant,stop_gained",
"frequency_reference_population": null,
"gene_hgnc_id": 28209,
"gene_symbol": "CEP19",
"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": "Pathogenic",
"phenotype_combined": "Bardet-Biedl syndrome",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.62,
"pos": 196707860,
"ref": "G",
"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_032898.5"
}
]
}