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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: 2-1648959-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=1648959&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 1648959,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_012293.3",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.2821G>A",
"hgvs_p": "p.Val941Met",
"transcript": "NM_012293.3",
"protein_id": "NP_036425.1",
"transcript_support_level": null,
"aa_start": 941,
"aa_end": null,
"aa_length": 1479,
"cds_start": 2821,
"cds_end": null,
"cds_length": 4440,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000252804.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_012293.3"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.2821G>A",
"hgvs_p": "p.Val941Met",
"transcript": "ENST00000252804.9",
"protein_id": "ENSP00000252804.4",
"transcript_support_level": 1,
"aa_start": 941,
"aa_end": null,
"aa_length": 1479,
"cds_start": 2821,
"cds_end": null,
"cds_length": 4440,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_012293.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000252804.9"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.2749G>A",
"hgvs_p": "p.Val917Met",
"transcript": "ENST00000857505.1",
"protein_id": "ENSP00000527564.1",
"transcript_support_level": null,
"aa_start": 917,
"aa_end": null,
"aa_length": 1455,
"cds_start": 2749,
"cds_end": null,
"cds_length": 4368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857505.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.2749G>A",
"hgvs_p": "p.Val917Met",
"transcript": "XM_005264707.4",
"protein_id": "XP_005264764.1",
"transcript_support_level": null,
"aa_start": 917,
"aa_end": null,
"aa_length": 1455,
"cds_start": 2749,
"cds_end": null,
"cds_length": 4368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005264707.4"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.2272G>A",
"hgvs_p": "p.Val758Met",
"transcript": "XM_011510396.2",
"protein_id": "XP_011508698.1",
"transcript_support_level": null,
"aa_start": 758,
"aa_end": null,
"aa_length": 1296,
"cds_start": 2272,
"cds_end": null,
"cds_length": 3891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510396.2"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.2272G>A",
"hgvs_p": "p.Val758Met",
"transcript": "XM_047445788.1",
"protein_id": "XP_047301744.1",
"transcript_support_level": null,
"aa_start": 758,
"aa_end": null,
"aa_length": 1296,
"cds_start": 2272,
"cds_end": null,
"cds_length": 3891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445788.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.2272G>A",
"hgvs_p": "p.Val758Met",
"transcript": "XM_047445789.1",
"protein_id": "XP_047301745.1",
"transcript_support_level": null,
"aa_start": 758,
"aa_end": null,
"aa_length": 1296,
"cds_start": 2272,
"cds_end": null,
"cds_length": 3891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445789.1"
},
{
"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": 15,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "n.2697-4207G>A",
"hgvs_p": null,
"transcript": "ENST00000478155.5",
"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": "retained_intron",
"feature": "ENST00000478155.5"
}
],
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"dbsnp": "rs189824177",
"frequency_reference_population": 0.0040401653,
"hom_count_reference_population": 21,
"allele_count_reference_population": 6494,
"gnomad_exomes_af": 0.00409974,
"gnomad_genomes_af": 0.00347035,
"gnomad_exomes_ac": 5966,
"gnomad_genomes_ac": 528,
"gnomad_exomes_homalt": 18,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00936591625213623,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.14,
"revel_prediction": "Benign",
"alphamissense_score": 0.3684,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.907,
"phylop100way_prediction": "Uncertain_significance",
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS1,BS2",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_012293.3",
"gene_symbol": "PXDN",
"hgnc_id": 14966,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2821G>A",
"hgvs_p": "p.Val941Met"
}
],
"clinvar_disease": "Anterior segment dysgenesis 7",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "Anterior segment dysgenesis 7",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}