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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: 2-1648590-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=1648590&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PXDN",
"hgnc_id": 14966,
"hgvs_c": "c.3190G>C",
"hgvs_p": "p.Ala1064Pro",
"inheritance_mode": "AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_012293.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_score": 4,
"allele_count_reference_population": 1,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.8828,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.04,
"chr": "2",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8885829448699951,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1479,
"aa_ref": "A",
"aa_start": 1064,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6817,
"cdna_start": 3250,
"cds_end": null,
"cds_length": 4440,
"cds_start": 3190,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_012293.3",
"gene_hgnc_id": 14966,
"gene_symbol": "PXDN",
"hgvs_c": "c.3190G>C",
"hgvs_p": "p.Ala1064Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000252804.9",
"protein_coding": true,
"protein_id": "NP_036425.1",
"strand": false,
"transcript": "NM_012293.3",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1479,
"aa_ref": "A",
"aa_start": 1064,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6817,
"cdna_start": 3250,
"cds_end": null,
"cds_length": 4440,
"cds_start": 3190,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000252804.9",
"gene_hgnc_id": 14966,
"gene_symbol": "PXDN",
"hgvs_c": "c.3190G>C",
"hgvs_p": "p.Ala1064Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_012293.3",
"protein_coding": true,
"protein_id": "ENSP00000252804.4",
"strand": false,
"transcript": "ENST00000252804.9",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1455,
"aa_ref": "A",
"aa_start": 1040,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7040,
"cdna_start": 3477,
"cds_end": null,
"cds_length": 4368,
"cds_start": 3118,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000857505.1",
"gene_hgnc_id": 14966,
"gene_symbol": "PXDN",
"hgvs_c": "c.3118G>C",
"hgvs_p": "p.Ala1040Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000527564.1",
"strand": false,
"transcript": "ENST00000857505.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1455,
"aa_ref": "A",
"aa_start": 1040,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6745,
"cdna_start": 3178,
"cds_end": null,
"cds_length": 4368,
"cds_start": 3118,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_005264707.4",
"gene_hgnc_id": 14966,
"gene_symbol": "PXDN",
"hgvs_c": "c.3118G>C",
"hgvs_p": "p.Ala1040Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005264764.1",
"strand": false,
"transcript": "XM_005264707.4",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1296,
"aa_ref": "A",
"aa_start": 881,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6655,
"cdna_start": 3088,
"cds_end": null,
"cds_length": 3891,
"cds_start": 2641,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "XM_011510396.2",
"gene_hgnc_id": 14966,
"gene_symbol": "PXDN",
"hgvs_c": "c.2641G>C",
"hgvs_p": "p.Ala881Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011508698.1",
"strand": false,
"transcript": "XM_011510396.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1296,
"aa_ref": "A",
"aa_start": 881,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6615,
"cdna_start": 3048,
"cds_end": null,
"cds_length": 3891,
"cds_start": 2641,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "XM_047445788.1",
"gene_hgnc_id": 14966,
"gene_symbol": "PXDN",
"hgvs_c": "c.2641G>C",
"hgvs_p": "p.Ala881Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047301744.1",
"strand": false,
"transcript": "XM_047445788.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1296,
"aa_ref": "A",
"aa_start": 881,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6579,
"cdna_start": 3012,
"cds_end": null,
"cds_length": 3891,
"cds_start": 2641,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_047445789.1",
"gene_hgnc_id": 14966,
"gene_symbol": "PXDN",
"hgvs_c": "c.2641G>C",
"hgvs_p": "p.Ala881Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047301745.1",
"strand": false,
"transcript": "XM_047445789.1",
"transcript_support_level": null
},
{
"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": 3840,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000478155.5",
"gene_hgnc_id": 14966,
"gene_symbol": "PXDN",
"hgvs_c": "n.2697-3838G>C",
"hgvs_p": null,
"intron_rank": 9,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000478155.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs202132697",
"effect": "missense_variant",
"frequency_reference_population": 6.8426317e-7,
"gene_hgnc_id": 14966,
"gene_symbol": "PXDN",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84263e-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": "Uncertain_significance",
"phylop100way_score": 4.774,
"pos": 1648590,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.538,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_012293.3"
}
]
}