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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: 22-43923921-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=43923921&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 43923921,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_025225.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA3",
"gene_hgnc_id": 18590,
"hgvs_c": "c.10G>A",
"hgvs_p": "p.Ala4Thr",
"transcript": "NM_025225.3",
"protein_id": "NP_079501.2",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 481,
"cds_start": 10,
"cds_end": null,
"cds_length": 1446,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000216180.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_025225.3"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA3",
"gene_hgnc_id": 18590,
"hgvs_c": "c.10G>A",
"hgvs_p": "p.Ala4Thr",
"transcript": "ENST00000216180.8",
"protein_id": "ENSP00000216180.3",
"transcript_support_level": 1,
"aa_start": 4,
"aa_end": null,
"aa_length": 481,
"cds_start": 10,
"cds_end": null,
"cds_length": 1446,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_025225.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000216180.8"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA3",
"gene_hgnc_id": 18590,
"hgvs_c": "c.10G>A",
"hgvs_p": "p.Ala4Thr",
"transcript": "ENST00000862822.1",
"protein_id": "ENSP00000532881.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 491,
"cds_start": 10,
"cds_end": null,
"cds_length": 1476,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862822.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA3",
"gene_hgnc_id": 18590,
"hgvs_c": "c.10G>A",
"hgvs_p": "p.Ala4Thr",
"transcript": "ENST00000862819.1",
"protein_id": "ENSP00000532878.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 489,
"cds_start": 10,
"cds_end": null,
"cds_length": 1470,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862819.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA3",
"gene_hgnc_id": 18590,
"hgvs_c": "c.10G>A",
"hgvs_p": "p.Ala4Thr",
"transcript": "ENST00000862820.1",
"protein_id": "ENSP00000532879.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 485,
"cds_start": 10,
"cds_end": null,
"cds_length": 1458,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862820.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA3",
"gene_hgnc_id": 18590,
"hgvs_c": "c.10G>A",
"hgvs_p": "p.Ala4Thr",
"transcript": "ENST00000423180.2",
"protein_id": "ENSP00000397987.2",
"transcript_support_level": 2,
"aa_start": 4,
"aa_end": null,
"aa_length": 477,
"cds_start": 10,
"cds_end": null,
"cds_length": 1434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000423180.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA3",
"gene_hgnc_id": 18590,
"hgvs_c": "c.10G>A",
"hgvs_p": "p.Ala4Thr",
"transcript": "ENST00000862821.1",
"protein_id": "ENSP00000532880.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 411,
"cds_start": 10,
"cds_end": null,
"cds_length": 1236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862821.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA3",
"gene_hgnc_id": 18590,
"hgvs_c": "c.10G>A",
"hgvs_p": "p.Ala4Thr",
"transcript": "ENST00000862823.1",
"protein_id": "ENSP00000532882.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 313,
"cds_start": 10,
"cds_end": null,
"cds_length": 942,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862823.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA3",
"gene_hgnc_id": 18590,
"hgvs_c": "n.10G>A",
"hgvs_p": null,
"transcript": "ENST00000406117.6",
"protein_id": "ENSP00000384668.2",
"transcript_support_level": 2,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000406117.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000304926",
"gene_hgnc_id": null,
"hgvs_c": "n.235+469C>T",
"hgvs_p": null,
"transcript": "ENST00000807134.1",
"protein_id": null,
"transcript_support_level": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000807134.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNPLA3",
"gene_hgnc_id": 18590,
"hgvs_c": "n.-193G>A",
"hgvs_p": null,
"transcript": "ENST00000478713.1",
"protein_id": null,
"transcript_support_level": 2,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000478713.1"
}
],
"gene_symbol": "PNPLA3",
"gene_hgnc_id": 18590,
"dbsnp": "rs778553702",
"frequency_reference_population": 0.0000014154563,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000141546,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.04764300584793091,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.11,
"revel_prediction": "Benign",
"alphamissense_score": 0.0854,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.73,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.463,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_025225.3",
"gene_symbol": "PNPLA3",
"hgnc_id": 18590,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.10G>A",
"hgvs_p": "p.Ala4Thr"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000807134.1",
"gene_symbol": "ENSG00000304926",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.235+469C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}