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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: 19-7555724-C-CGCCA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=7555724&ref=C&alt=CGCCA&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 7555724,
"ref": "C",
"alt": "CGCCA",
"effect": "frameshift_variant",
"transcript": "ENST00000600737.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "QP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3058_3061dupAGCC",
"hgvs_p": "p.Arg1021fs",
"transcript": "NM_001166114.2",
"protein_id": "NP_001159586.1",
"transcript_support_level": null,
"aa_start": 1021,
"aa_end": null,
"aa_length": 1365,
"cds_start": 3062,
"cds_end": null,
"cds_length": 4098,
"cdna_start": 3134,
"cdna_end": null,
"cdna_length": 4372,
"mane_select": "ENST00000600737.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "QP?",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3058_3061dupAGCC",
"hgvs_p": "p.Arg1021fs",
"transcript": "ENST00000600737.6",
"protein_id": "ENSP00000473211.1",
"transcript_support_level": 1,
"aa_start": 1021,
"aa_end": null,
"aa_length": 1365,
"cds_start": 3062,
"cds_end": null,
"cds_length": 4098,
"cdna_start": 3134,
"cdna_end": null,
"cdna_length": 4372,
"mane_select": "NM_001166114.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "QP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.2944_2947dupAGCC",
"hgvs_p": "p.Arg983fs",
"transcript": "ENST00000221249.10",
"protein_id": "ENSP00000221249.5",
"transcript_support_level": 1,
"aa_start": 983,
"aa_end": null,
"aa_length": 1327,
"cds_start": 2948,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 3379,
"cdna_end": null,
"cdna_length": 4617,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "QP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.2944_2947dupAGCC",
"hgvs_p": "p.Arg983fs",
"transcript": "ENST00000450331.7",
"protein_id": "ENSP00000394348.2",
"transcript_support_level": 1,
"aa_start": 983,
"aa_end": null,
"aa_length": 1327,
"cds_start": 2948,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 3219,
"cdna_end": null,
"cdna_length": 4457,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "QP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3088_3091dupAGCC",
"hgvs_p": "p.Arg1031fs",
"transcript": "NM_001166111.2",
"protein_id": "NP_001159583.1",
"transcript_support_level": null,
"aa_start": 1031,
"aa_end": null,
"aa_length": 1375,
"cds_start": 3092,
"cds_end": null,
"cds_length": 4128,
"cdna_start": 3298,
"cdna_end": null,
"cdna_length": 4536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "QP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3088_3091dupAGCC",
"hgvs_p": "p.Arg1031fs",
"transcript": "ENST00000414982.7",
"protein_id": "ENSP00000407509.2",
"transcript_support_level": 2,
"aa_start": 1031,
"aa_end": null,
"aa_length": 1375,
"cds_start": 3092,
"cds_end": null,
"cds_length": 4128,
"cdna_start": 3287,
"cdna_end": null,
"cdna_length": 4522,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "QP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.2944_2947dupAGCC",
"hgvs_p": "p.Arg983fs",
"transcript": "NM_001166113.1",
"protein_id": "NP_001159585.1",
"transcript_support_level": null,
"aa_start": 983,
"aa_end": null,
"aa_length": 1327,
"cds_start": 2948,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 3219,
"cdna_end": null,
"cdna_length": 4460,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "QP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.2944_2947dupAGCC",
"hgvs_p": "p.Arg983fs",
"transcript": "NM_006702.5",
"protein_id": "NP_006693.3",
"transcript_support_level": null,
"aa_start": 983,
"aa_end": null,
"aa_length": 1327,
"cds_start": 2948,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 3219,
"cdna_end": null,
"cdna_length": 4457,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "QP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.2863_2866dupAGCC",
"hgvs_p": "p.Arg956fs",
"transcript": "NM_001166112.2",
"protein_id": "NP_001159584.1",
"transcript_support_level": null,
"aa_start": 956,
"aa_end": null,
"aa_length": 1300,
"cds_start": 2867,
"cds_end": null,
"cds_length": 3903,
"cdna_start": 3267,
"cdna_end": null,
"cdna_length": 4505,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "QP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.2863_2866dupAGCC",
"hgvs_p": "p.Arg956fs",
"transcript": "ENST00000545201.6",
"protein_id": "ENSP00000443323.1",
"transcript_support_level": 2,
"aa_start": 956,
"aa_end": null,
"aa_length": 1300,
"cds_start": 2867,
"cds_end": null,
"cds_length": 3903,
"cdna_start": 3267,
"cdna_end": null,
"cdna_length": 4502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "QP?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.229_232dupAGCC",
"hgvs_p": "p.Arg78fs",
"transcript": "ENST00000646984.1",
"protein_id": "ENSP00000496219.1",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 223,
"cds_start": 233,
"cds_end": null,
"cds_length": 672,
"cdna_start": 233,
"cdna_end": null,
"cdna_length": 672,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"dbsnp": "rs606231167",
"frequency_reference_population": 0.00016484184,
"hom_count_reference_population": 0,
"allele_count_reference_population": 266,
"gnomad_exomes_af": 0.000169001,
"gnomad_genomes_af": 0.000124887,
"gnomad_exomes_ac": 247,
"gnomad_genomes_ac": 19,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 2.078,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000600737.6",
"gene_symbol": "PNPLA6",
"hgnc_id": 16268,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3058_3061dupAGCC",
"hgvs_p": "p.Arg1021fs"
}
],
"clinvar_disease": "Ataxia-hypogonadism-choroidal dystrophy syndrome,Hereditary spastic paraplegia,Hereditary spastic paraplegia 39,Inborn genetic diseases,Laurence-Moon syndrome,PNPLA6-related disorder,Retinal dystrophy,Trichomegaly-retina pigmentary degeneration-dwarfism syndrome,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:12 O:1",
"phenotype_combined": "Hereditary spastic paraplegia 39|Laurence-Moon syndrome|Trichomegaly-retina pigmentary degeneration-dwarfism syndrome|PNPLA6-related disorder|Ataxia-hypogonadism-choroidal dystrophy syndrome|Inborn genetic diseases|Ataxia-hypogonadism-choroidal dystrophy syndrome;Hereditary spastic paraplegia 39;Trichomegaly-retina pigmentary degeneration-dwarfism syndrome;Laurence-Moon syndrome|not provided|Retinal dystrophy|Hereditary spastic paraplegia",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}