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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: 19-7555609-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=7555609&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 7555609,
"ref": "G",
"alt": "C",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000600737.6",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_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.2939G>C",
"hgvs_p": "p.Gly980Ala",
"transcript": "NM_001166114.2",
"protein_id": "NP_001159586.1",
"transcript_support_level": null,
"aa_start": 980,
"aa_end": null,
"aa_length": 1365,
"cds_start": 2939,
"cds_end": null,
"cds_length": 4098,
"cdna_start": 3011,
"cdna_end": null,
"cdna_length": 4372,
"mane_select": "ENST00000600737.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_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.2939G>C",
"hgvs_p": "p.Gly980Ala",
"transcript": "ENST00000600737.6",
"protein_id": "ENSP00000473211.1",
"transcript_support_level": 1,
"aa_start": 980,
"aa_end": null,
"aa_length": 1365,
"cds_start": 2939,
"cds_end": null,
"cds_length": 4098,
"cdna_start": 3011,
"cdna_end": null,
"cdna_length": 4372,
"mane_select": "NM_001166114.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_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.2825G>C",
"hgvs_p": "p.Gly942Ala",
"transcript": "ENST00000221249.10",
"protein_id": "ENSP00000221249.5",
"transcript_support_level": 1,
"aa_start": 942,
"aa_end": null,
"aa_length": 1327,
"cds_start": 2825,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 3256,
"cdna_end": null,
"cdna_length": 4617,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_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.2825G>C",
"hgvs_p": "p.Gly942Ala",
"transcript": "ENST00000450331.7",
"protein_id": "ENSP00000394348.2",
"transcript_support_level": 1,
"aa_start": 942,
"aa_end": null,
"aa_length": 1327,
"cds_start": 2825,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 3096,
"cdna_end": null,
"cdna_length": 4457,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_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.2969G>C",
"hgvs_p": "p.Gly990Ala",
"transcript": "NM_001166111.2",
"protein_id": "NP_001159583.1",
"transcript_support_level": null,
"aa_start": 990,
"aa_end": null,
"aa_length": 1375,
"cds_start": 2969,
"cds_end": null,
"cds_length": 4128,
"cdna_start": 3175,
"cdna_end": null,
"cdna_length": 4536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_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.2969G>C",
"hgvs_p": "p.Gly990Ala",
"transcript": "ENST00000414982.7",
"protein_id": "ENSP00000407509.2",
"transcript_support_level": 2,
"aa_start": 990,
"aa_end": null,
"aa_length": 1375,
"cds_start": 2969,
"cds_end": null,
"cds_length": 4128,
"cdna_start": 3164,
"cdna_end": null,
"cdna_length": 4522,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_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.2825G>C",
"hgvs_p": "p.Gly942Ala",
"transcript": "NM_001166113.1",
"protein_id": "NP_001159585.1",
"transcript_support_level": null,
"aa_start": 942,
"aa_end": null,
"aa_length": 1327,
"cds_start": 2825,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 3096,
"cdna_end": null,
"cdna_length": 4460,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_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.2825G>C",
"hgvs_p": "p.Gly942Ala",
"transcript": "NM_006702.5",
"protein_id": "NP_006693.3",
"transcript_support_level": null,
"aa_start": 942,
"aa_end": null,
"aa_length": 1327,
"cds_start": 2825,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 3096,
"cdna_end": null,
"cdna_length": 4457,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_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.2744G>C",
"hgvs_p": "p.Gly915Ala",
"transcript": "NM_001166112.2",
"protein_id": "NP_001159584.1",
"transcript_support_level": null,
"aa_start": 915,
"aa_end": null,
"aa_length": 1300,
"cds_start": 2744,
"cds_end": null,
"cds_length": 3903,
"cdna_start": 3144,
"cdna_end": null,
"cdna_length": 4505,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_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.2744G>C",
"hgvs_p": "p.Gly915Ala",
"transcript": "ENST00000545201.6",
"protein_id": "ENSP00000443323.1",
"transcript_support_level": 2,
"aa_start": 915,
"aa_end": null,
"aa_length": 1300,
"cds_start": 2744,
"cds_end": null,
"cds_length": 3903,
"cdna_start": 3144,
"cdna_end": null,
"cdna_length": 4502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_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.110G>C",
"hgvs_p": "p.Gly37Ala",
"transcript": "ENST00000646984.1",
"protein_id": "ENSP00000496219.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 223,
"cds_start": 110,
"cds_end": null,
"cds_length": 672,
"cdna_start": 110,
"cdna_end": null,
"cdna_length": 672,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"dbsnp": "rs201902695",
"frequency_reference_population": 0.00012597397,
"hom_count_reference_population": 1,
"allele_count_reference_population": 203,
"gnomad_exomes_af": 0.00012883,
"gnomad_genomes_af": 0.0000985791,
"gnomad_exomes_ac": 188,
"gnomad_genomes_ac": 15,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.29246222972869873,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.899,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9695,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.35,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.781,
"phylop100way_prediction": "Pathogenic",
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP2,PP3,BP4",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 1,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP2",
"PP3",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000600737.6",
"gene_symbol": "PNPLA6",
"hgnc_id": 16268,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2939G>C",
"hgvs_p": "p.Gly980Ala"
}
],
"clinvar_disease": "Hereditary spastic paraplegia 39,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:5 LB:1",
"phenotype_combined": "Hereditary spastic paraplegia 39|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}