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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: 19-7561488-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=7561488&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM1",
"PM2",
"PP2",
"BP4"
],
"effects": [
"missense_variant",
"splice_region_variant"
],
"gene_symbol": "PNPLA6",
"hgnc_id": 16268,
"hgvs_c": "c.4054G>A",
"hgvs_p": "p.Glu1352Lys",
"inheritance_mode": "AR",
"pathogenic_score": 5,
"score": 4,
"transcript": "NM_001166111.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PM2,PP2,BP4",
"acmg_score": 4,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.1552,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.39,
"chr": "19",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.2792441248893738,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1365,
"aa_ref": "E",
"aa_start": 1342,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4372,
"cdna_start": 4096,
"cds_end": null,
"cds_length": 4098,
"cds_start": 4024,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 32,
"exon_rank": 32,
"exon_rank_end": null,
"feature": "NM_001166114.2",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.4024G>A",
"hgvs_p": "p.Glu1342Lys",
"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": "K",
"aa_end": null,
"aa_length": 1365,
"aa_ref": "E",
"aa_start": 1342,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4372,
"cdna_start": 4096,
"cds_end": null,
"cds_length": 4098,
"cds_start": 4024,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 32,
"exon_rank": 32,
"exon_rank_end": null,
"feature": "ENST00000600737.6",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.4024G>A",
"hgvs_p": "p.Glu1342Lys",
"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": "K",
"aa_end": null,
"aa_length": 1327,
"aa_ref": "E",
"aa_start": 1304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4617,
"cdna_start": 4341,
"cds_end": null,
"cds_length": 3984,
"cds_start": 3910,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 35,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "ENST00000221249.10",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.3910G>A",
"hgvs_p": "p.Glu1304Lys",
"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": "K",
"aa_end": null,
"aa_length": 1327,
"aa_ref": "E",
"aa_start": 1304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4457,
"cdna_start": 4181,
"cds_end": null,
"cds_length": 3984,
"cds_start": 3910,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 35,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "ENST00000450331.7",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.3910G>A",
"hgvs_p": "p.Glu1304Lys",
"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": "K",
"aa_end": null,
"aa_length": 1375,
"aa_ref": "E",
"aa_start": 1352,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4536,
"cdna_start": 4260,
"cds_end": null,
"cds_length": 4128,
"cds_start": 4054,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 34,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "NM_001166111.2",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.4054G>A",
"hgvs_p": "p.Glu1352Lys",
"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": "K",
"aa_end": null,
"aa_length": 1375,
"aa_ref": "E",
"aa_start": 1352,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4522,
"cdna_start": 4249,
"cds_end": null,
"cds_length": 4128,
"cds_start": 4054,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 34,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000414982.7",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.4054G>A",
"hgvs_p": "p.Glu1352Lys",
"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": "K",
"aa_end": null,
"aa_length": 1327,
"aa_ref": "E",
"aa_start": 1304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4460,
"cdna_start": 4181,
"cds_end": null,
"cds_length": 3984,
"cds_start": 3910,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 35,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "NM_001166113.1",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.3910G>A",
"hgvs_p": "p.Glu1304Lys",
"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": "K",
"aa_end": null,
"aa_length": 1327,
"aa_ref": "E",
"aa_start": 1304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4457,
"cdna_start": 4181,
"cds_end": null,
"cds_length": 3984,
"cds_start": 3910,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 35,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "NM_006702.5",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.3910G>A",
"hgvs_p": "p.Glu1304Lys",
"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": "K",
"aa_end": null,
"aa_length": 1300,
"aa_ref": "E",
"aa_start": 1277,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4505,
"cdna_start": 4229,
"cds_end": null,
"cds_length": 3903,
"cds_start": 3829,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 34,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "NM_001166112.2",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.3829G>A",
"hgvs_p": "p.Glu1277Lys",
"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": "K",
"aa_end": null,
"aa_length": 1300,
"aa_ref": "E",
"aa_start": 1277,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4502,
"cdna_start": 4229,
"cds_end": null,
"cds_length": 3903,
"cds_start": 3829,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 34,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000545201.6",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.3829G>A",
"hgvs_p": "p.Glu1277Lys",
"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": "K",
"aa_end": null,
"aa_length": 154,
"aa_ref": "E",
"aa_start": 131,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 669,
"cdna_start": 393,
"cds_end": null,
"cds_length": 465,
"cds_start": 391,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000599947.1",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "c.391G>A",
"hgvs_p": "p.Glu131Lys",
"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
},
{
"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": 658,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000597202.1",
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"hgvs_c": "n.382G>A",
"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": "ENST00000597202.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.0711617655946594,
"dbsnp": "rs12974798",
"effect": "missense_variant,splice_region_variant",
"frequency_reference_population": 6.886417e-7,
"gene_hgnc_id": 16268,
"gene_symbol": "PNPLA6",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.88642e-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": 2.347,
"pos": 7561488,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.174,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.30000001192092896,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.51,
"transcript": "NM_001166111.2"
}
]
}