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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: 19-7540675-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=7540675&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 7540675,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001166111.2",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.760G>A",
"hgvs_p": "p.Val254Ile",
"transcript": "NM_001166114.2",
"protein_id": "NP_001159586.1",
"transcript_support_level": null,
"aa_start": 254,
"aa_end": null,
"aa_length": 1365,
"cds_start": 760,
"cds_end": null,
"cds_length": 4098,
"cdna_start": 832,
"cdna_end": null,
"cdna_length": 4372,
"mane_select": "ENST00000600737.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001166114.2"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.760G>A",
"hgvs_p": "p.Val254Ile",
"transcript": "ENST00000600737.6",
"protein_id": "ENSP00000473211.1",
"transcript_support_level": 1,
"aa_start": 254,
"aa_end": null,
"aa_length": 1365,
"cds_start": 760,
"cds_end": null,
"cds_length": 4098,
"cdna_start": 832,
"cdna_end": null,
"cdna_length": 4372,
"mane_select": "NM_001166114.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000600737.6"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.643G>A",
"hgvs_p": "p.Val215Ile",
"transcript": "ENST00000221249.10",
"protein_id": "ENSP00000221249.5",
"transcript_support_level": 1,
"aa_start": 215,
"aa_end": null,
"aa_length": 1327,
"cds_start": 643,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 1074,
"cdna_end": null,
"cdna_length": 4617,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000221249.10"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.643G>A",
"hgvs_p": "p.Val215Ile",
"transcript": "ENST00000450331.7",
"protein_id": "ENSP00000394348.2",
"transcript_support_level": 1,
"aa_start": 215,
"aa_end": null,
"aa_length": 1327,
"cds_start": 643,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 914,
"cdna_end": null,
"cdna_length": 4457,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000450331.7"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.787G>A",
"hgvs_p": "p.Val263Ile",
"transcript": "NM_001166111.2",
"protein_id": "NP_001159583.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 1375,
"cds_start": 787,
"cds_end": null,
"cds_length": 4128,
"cdna_start": 993,
"cdna_end": null,
"cdna_length": 4536,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001166111.2"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.787G>A",
"hgvs_p": "p.Val263Ile",
"transcript": "ENST00000414982.7",
"protein_id": "ENSP00000407509.2",
"transcript_support_level": 2,
"aa_start": 263,
"aa_end": null,
"aa_length": 1375,
"cds_start": 787,
"cds_end": null,
"cds_length": 4128,
"cdna_start": 982,
"cdna_end": null,
"cdna_length": 4522,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000414982.7"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.643G>A",
"hgvs_p": "p.Val215Ile",
"transcript": "NM_001166113.1",
"protein_id": "NP_001159585.1",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 1327,
"cds_start": 643,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 914,
"cdna_end": null,
"cdna_length": 4460,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001166113.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.643G>A",
"hgvs_p": "p.Val215Ile",
"transcript": "NM_006702.5",
"protein_id": "NP_006693.3",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 1327,
"cds_start": 643,
"cds_end": null,
"cds_length": 3984,
"cdna_start": 914,
"cdna_end": null,
"cdna_length": 4457,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006702.5"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.643G>A",
"hgvs_p": "p.Val215Ile",
"transcript": "NM_001166112.2",
"protein_id": "NP_001159584.1",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 1300,
"cds_start": 643,
"cds_end": null,
"cds_length": 3903,
"cdna_start": 1043,
"cdna_end": null,
"cdna_length": 4505,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001166112.2"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.643G>A",
"hgvs_p": "p.Val215Ile",
"transcript": "ENST00000545201.6",
"protein_id": "ENSP00000443323.1",
"transcript_support_level": 2,
"aa_start": 215,
"aa_end": null,
"aa_length": 1300,
"cds_start": 643,
"cds_end": null,
"cds_length": 3903,
"cdna_start": 1043,
"cdna_end": null,
"cdna_length": 4502,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000545201.6"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.280G>A",
"hgvs_p": "p.Val94Ile",
"transcript": "ENST00000595264.5",
"protein_id": "ENSP00000472456.1",
"transcript_support_level": 3,
"aa_start": 94,
"aa_end": null,
"aa_length": 265,
"cds_start": 280,
"cds_end": null,
"cds_length": 798,
"cdna_start": 282,
"cdna_end": null,
"cdna_length": 800,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000595264.5"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"hgvs_c": "c.226G>A",
"hgvs_p": "p.Val76Ile",
"transcript": "ENST00000594551.1",
"protein_id": "ENSP00000470060.1",
"transcript_support_level": 4,
"aa_start": 76,
"aa_end": null,
"aa_length": 190,
"cds_start": 226,
"cds_end": null,
"cds_length": 573,
"cdna_start": 227,
"cdna_end": null,
"cdna_length": 574,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000594551.1"
},
{
"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.551G>A",
"hgvs_p": null,
"transcript": "ENST00000598462.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 585,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000598462.1"
}
],
"gene_symbol": "PNPLA6",
"gene_hgnc_id": 16268,
"dbsnp": "rs587777184",
"frequency_reference_population": 0.0000041048374,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000410484,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7637829780578613,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.861,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1217,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 10.003,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP2,PP3",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001166111.2",
"gene_symbol": "PNPLA6",
"hgnc_id": 16268,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.787G>A",
"hgvs_p": "p.Val263Ile"
}
],
"clinvar_disease": "Hereditary spastic paraplegia 39,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1 O:1",
"phenotype_combined": "Hereditary spastic paraplegia 39|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}