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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: 19-7561542-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=7561542&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 7561542,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000600737.6",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.4078G>A",
"hgvs_p": "p.Gly1360Ser",
"transcript": "NM_001166114.2",
"protein_id": "NP_001159586.1",
"transcript_support_level": null,
"aa_start": 1360,
"aa_end": null,
"aa_length": 1365,
"cds_start": 4078,
"cds_end": null,
"cds_length": 4098,
"cdna_start": 4150,
"cdna_end": null,
"cdna_length": 4372,
"mane_select": "ENST00000600737.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.4078G>A",
"hgvs_p": "p.Gly1360Ser",
"transcript": "ENST00000600737.6",
"protein_id": "ENSP00000473211.1",
"transcript_support_level": 1,
"aa_start": 1360,
"aa_end": null,
"aa_length": 1365,
"cds_start": 4078,
"cds_end": null,
"cds_length": 4098,
"cdna_start": 4150,
"cdna_end": null,
"cdna_length": 4372,
"mane_select": "NM_001166114.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3964G>A",
"hgvs_p": "p.Gly1322Ser",
"transcript": "ENST00000221249.10",
"protein_id": "ENSP00000221249.5",
"transcript_support_level": 1,
"aa_start": 1322,
"aa_end": null,
"aa_length": 1327,
"cds_start": 3964,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 4395,
"cdna_end": null,
"cdna_length": 4617,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3964G>A",
"hgvs_p": "p.Gly1322Ser",
"transcript": "ENST00000450331.7",
"protein_id": "ENSP00000394348.2",
"transcript_support_level": 1,
"aa_start": 1322,
"aa_end": null,
"aa_length": 1327,
"cds_start": 3964,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 4235,
"cdna_end": null,
"cdna_length": 4457,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.4108G>A",
"hgvs_p": "p.Gly1370Ser",
"transcript": "NM_001166111.2",
"protein_id": "NP_001159583.1",
"transcript_support_level": null,
"aa_start": 1370,
"aa_end": null,
"aa_length": 1375,
"cds_start": 4108,
"cds_end": null,
"cds_length": 4128,
"cdna_start": 4314,
"cdna_end": null,
"cdna_length": 4536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.4108G>A",
"hgvs_p": "p.Gly1370Ser",
"transcript": "ENST00000414982.7",
"protein_id": "ENSP00000407509.2",
"transcript_support_level": 2,
"aa_start": 1370,
"aa_end": null,
"aa_length": 1375,
"cds_start": 4108,
"cds_end": null,
"cds_length": 4128,
"cdna_start": 4303,
"cdna_end": null,
"cdna_length": 4522,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3964G>A",
"hgvs_p": "p.Gly1322Ser",
"transcript": "NM_001166113.1",
"protein_id": "NP_001159585.1",
"transcript_support_level": null,
"aa_start": 1322,
"aa_end": null,
"aa_length": 1327,
"cds_start": 3964,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 4235,
"cdna_end": null,
"cdna_length": 4460,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3964G>A",
"hgvs_p": "p.Gly1322Ser",
"transcript": "NM_006702.5",
"protein_id": "NP_006693.3",
"transcript_support_level": null,
"aa_start": 1322,
"aa_end": null,
"aa_length": 1327,
"cds_start": 3964,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 4235,
"cdna_end": null,
"cdna_length": 4457,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3883G>A",
"hgvs_p": "p.Gly1295Ser",
"transcript": "NM_001166112.2",
"protein_id": "NP_001159584.1",
"transcript_support_level": null,
"aa_start": 1295,
"aa_end": null,
"aa_length": 1300,
"cds_start": 3883,
"cds_end": null,
"cds_length": 3903,
"cdna_start": 4283,
"cdna_end": null,
"cdna_length": 4505,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.3883G>A",
"hgvs_p": "p.Gly1295Ser",
"transcript": "ENST00000545201.6",
"protein_id": "ENSP00000443323.1",
"transcript_support_level": 2,
"aa_start": 1295,
"aa_end": null,
"aa_length": 1300,
"cds_start": 3883,
"cds_end": null,
"cds_length": 3903,
"cdna_start": 4283,
"cdna_end": null,
"cdna_length": 4502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.445G>A",
"hgvs_p": "p.Gly149Ser",
"transcript": "ENST00000599947.1",
"protein_id": "ENSP00000469171.1",
"transcript_support_level": 2,
"aa_start": 149,
"aa_end": null,
"aa_length": 154,
"cds_start": 445,
"cds_end": null,
"cds_length": 465,
"cdna_start": 447,
"cdna_end": null,
"cdna_length": 669,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "n.436G>A",
"hgvs_p": null,
"transcript": "ENST00000597202.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 658,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"dbsnp": "rs145178162",
"frequency_reference_population": 0.0060151303,
"hom_count_reference_population": 34,
"allele_count_reference_population": 9659,
"gnomad_exomes_af": 0.00616375,
"gnomad_genomes_af": 0.00459661,
"gnomad_exomes_ac": 8959,
"gnomad_genomes_ac": 700,
"gnomad_exomes_homalt": 32,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00409698486328125,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.011,
"revel_prediction": "Benign",
"alphamissense_score": 0.0675,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.68,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.285,
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "PP2,BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 20,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000600737.6",
"gene_symbol": "PNPLA6",
"hgnc_id": 16268,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4078G>A",
"hgvs_p": "p.Gly1360Ser"
}
],
"clinvar_disease": "Hereditary spastic paraplegia,Hereditary spastic paraplegia 39,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:5",
"phenotype_combined": "not provided|not specified|Hereditary spastic paraplegia 39|Hereditary spastic paraplegia",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}