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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: 19-7558861-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=7558861&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM1",
"PM2",
"PP2",
"PP3_Moderate",
"PP5_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PNPLA6",
"hgnc_id": 16268,
"hgvs_c": "c.3439C>T",
"hgvs_p": "p.Arg1147Cys",
"inheritance_mode": "AR",
"pathogenic_score": 13,
"score": 13,
"transcript": "NM_001166111.2",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PM2,PP2,PP3_Moderate,PP5_Moderate",
"acmg_score": 13,
"allele_count_reference_population": 25,
"alphamissense_prediction": null,
"alphamissense_score": 0.1661,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.31,
"chr": "19",
"clinvar_classification": "Likely pathogenic",
"clinvar_disease": "Ataxia-hypogonadism-choroidal dystrophy syndrome,Hereditary spastic paraplegia 39",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8955395221710205,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1365,
"aa_ref": "R",
"aa_start": 1137,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4372,
"cdna_start": 3481,
"cds_end": null,
"cds_length": 4098,
"cds_start": 3409,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "NM_001166114.2",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.3409C>T",
"hgvs_p": "p.Arg1137Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000600737.6",
"protein_coding": true,
"protein_id": "NP_001159586.1",
"strand": true,
"transcript": "NM_001166114.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1365,
"aa_ref": "R",
"aa_start": 1137,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4372,
"cdna_start": 3481,
"cds_end": null,
"cds_length": 4098,
"cds_start": 3409,
"consequences": [
"missense_variant"
],
"exon_count": 32,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000600737.6",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.3409C>T",
"hgvs_p": "p.Arg1137Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001166114.2",
"protein_coding": true,
"protein_id": "ENSP00000473211.1",
"strand": true,
"transcript": "ENST00000600737.6",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1327,
"aa_ref": "R",
"aa_start": 1099,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4617,
"cdna_start": 3726,
"cds_end": null,
"cds_length": 3984,
"cds_start": 3295,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 31,
"exon_rank_end": null,
"feature": "ENST00000221249.10",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.3295C>T",
"hgvs_p": "p.Arg1099Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000221249.5",
"strand": true,
"transcript": "ENST00000221249.10",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1327,
"aa_ref": "R",
"aa_start": 1099,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4457,
"cdna_start": 3566,
"cds_end": null,
"cds_length": 3984,
"cds_start": 3295,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 31,
"exon_rank_end": null,
"feature": "ENST00000450331.7",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.3295C>T",
"hgvs_p": "p.Arg1099Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000394348.2",
"strand": true,
"transcript": "ENST00000450331.7",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1375,
"aa_ref": "R",
"aa_start": 1147,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4536,
"cdna_start": 3645,
"cds_end": null,
"cds_length": 4128,
"cds_start": 3439,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 30,
"exon_rank_end": null,
"feature": "NM_001166111.2",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.3439C>T",
"hgvs_p": "p.Arg1147Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001159583.1",
"strand": true,
"transcript": "NM_001166111.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1375,
"aa_ref": "R",
"aa_start": 1147,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4522,
"cdna_start": 3634,
"cds_end": null,
"cds_length": 4128,
"cds_start": 3439,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 30,
"exon_rank_end": null,
"feature": "ENST00000414982.7",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.3439C>T",
"hgvs_p": "p.Arg1147Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000407509.2",
"strand": true,
"transcript": "ENST00000414982.7",
"transcript_support_level": 2
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1327,
"aa_ref": "R",
"aa_start": 1099,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4460,
"cdna_start": 3566,
"cds_end": null,
"cds_length": 3984,
"cds_start": 3295,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 31,
"exon_rank_end": null,
"feature": "NM_001166113.1",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.3295C>T",
"hgvs_p": "p.Arg1099Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001159585.1",
"strand": true,
"transcript": "NM_001166113.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1327,
"aa_ref": "R",
"aa_start": 1099,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4457,
"cdna_start": 3566,
"cds_end": null,
"cds_length": 3984,
"cds_start": 3295,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 31,
"exon_rank_end": null,
"feature": "NM_006702.5",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.3295C>T",
"hgvs_p": "p.Arg1099Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_006693.3",
"strand": true,
"transcript": "NM_006702.5",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1300,
"aa_ref": "R",
"aa_start": 1072,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4505,
"cdna_start": 3614,
"cds_end": null,
"cds_length": 3903,
"cds_start": 3214,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 30,
"exon_rank_end": null,
"feature": "NM_001166112.2",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.3214C>T",
"hgvs_p": "p.Arg1072Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001159584.1",
"strand": true,
"transcript": "NM_001166112.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1300,
"aa_ref": "R",
"aa_start": 1072,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4502,
"cdna_start": 3614,
"cds_end": null,
"cds_length": 3903,
"cds_start": 3214,
"consequences": [
"missense_variant"
],
"exon_count": 34,
"exon_rank": 30,
"exon_rank_end": null,
"feature": "ENST00000545201.6",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.3214C>T",
"hgvs_p": "p.Arg1072Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000443323.1",
"strand": true,
"transcript": "ENST00000545201.6",
"transcript_support_level": 2
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 223,
"aa_ref": "R",
"aa_start": 194,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 672,
"cdna_start": 580,
"cds_end": null,
"cds_length": 672,
"cds_start": 580,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000646984.1",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.580C>T",
"hgvs_p": "p.Arg194Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000496219.1",
"strand": true,
"transcript": "ENST00000646984.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 154,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 669,
"cdna_start": null,
"cds_end": null,
"cds_length": 465,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000599947.1",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.-108C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000469171.1",
"strand": true,
"transcript": "ENST00000599947.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs587777854",
"effect": "missense_variant",
"frequency_reference_population": 0.000015534955,
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"gnomad_exomes_ac": 21,
"gnomad_exomes_af": 0.0000144121,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.0000262871,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely pathogenic",
"phenotype_combined": "Ataxia-hypogonadism-choroidal dystrophy syndrome|Hereditary spastic paraplegia 39",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.244,
"pos": 7558861,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.805,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001166111.2"
}
]
}