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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: 1-116395247-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=116395247&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 116395247,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000295598.10",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A1",
"gene_hgnc_id": 799,
"hgvs_c": "c.1798C>A",
"hgvs_p": "p.Pro600Thr",
"transcript": "NM_000701.8",
"protein_id": "NP_000692.2",
"transcript_support_level": null,
"aa_start": 600,
"aa_end": null,
"aa_length": 1023,
"cds_start": 1798,
"cds_end": null,
"cds_length": 3072,
"cdna_start": 2066,
"cdna_end": null,
"cdna_length": 3670,
"mane_select": "ENST00000295598.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A1",
"gene_hgnc_id": 799,
"hgvs_c": "c.1798C>A",
"hgvs_p": "p.Pro600Thr",
"transcript": "ENST00000295598.10",
"protein_id": "ENSP00000295598.5",
"transcript_support_level": 1,
"aa_start": 600,
"aa_end": null,
"aa_length": 1023,
"cds_start": 1798,
"cds_end": null,
"cds_length": 3072,
"cdna_start": 2066,
"cdna_end": null,
"cdna_length": 3670,
"mane_select": "NM_000701.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "ATP1A1-AS1",
"gene_hgnc_id": 28262,
"hgvs_c": "n.411-2221G>T",
"hgvs_p": null,
"transcript": "ENST00000608511.6",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2862,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A1",
"gene_hgnc_id": 799,
"hgvs_c": "c.1798C>A",
"hgvs_p": "p.Pro600Thr",
"transcript": "NM_001160233.2",
"protein_id": "NP_001153705.1",
"transcript_support_level": null,
"aa_start": 600,
"aa_end": null,
"aa_length": 1023,
"cds_start": 1798,
"cds_end": null,
"cds_length": 3072,
"cdna_start": 2161,
"cdna_end": null,
"cdna_length": 3765,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A1",
"gene_hgnc_id": 799,
"hgvs_c": "c.1798C>A",
"hgvs_p": "p.Pro600Thr",
"transcript": "ENST00000537345.5",
"protein_id": "ENSP00000445306.1",
"transcript_support_level": 2,
"aa_start": 600,
"aa_end": null,
"aa_length": 1023,
"cds_start": 1798,
"cds_end": null,
"cds_length": 3072,
"cdna_start": 2161,
"cdna_end": null,
"cdna_length": 3763,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A1",
"gene_hgnc_id": 799,
"hgvs_c": "c.1705C>A",
"hgvs_p": "p.Pro569Thr",
"transcript": "NM_001160234.2",
"protein_id": "NP_001153706.1",
"transcript_support_level": null,
"aa_start": 569,
"aa_end": null,
"aa_length": 992,
"cds_start": 1705,
"cds_end": null,
"cds_length": 2979,
"cdna_start": 1970,
"cdna_end": null,
"cdna_length": 3574,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A1",
"gene_hgnc_id": 799,
"hgvs_c": "c.1705C>A",
"hgvs_p": "p.Pro569Thr",
"transcript": "ENST00000369496.8",
"protein_id": "ENSP00000358508.4",
"transcript_support_level": 2,
"aa_start": 569,
"aa_end": null,
"aa_length": 992,
"cds_start": 1705,
"cds_end": null,
"cds_length": 2979,
"cdna_start": 1970,
"cdna_end": null,
"cdna_length": 3572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "ATP1A1-AS1",
"gene_hgnc_id": 28262,
"hgvs_c": "n.657-2221G>T",
"hgvs_p": null,
"transcript": "ENST00000674941.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3122,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ATP1A1-AS1",
"gene_hgnc_id": 28262,
"hgvs_c": "n.184-2221G>T",
"hgvs_p": null,
"transcript": "ENST00000675524.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2639,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ATP1A1-AS1",
"gene_hgnc_id": 28262,
"hgvs_c": "n.385+5649G>T",
"hgvs_p": null,
"transcript": "ENST00000675607.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1014,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ATP1A1-AS1",
"gene_hgnc_id": 28262,
"hgvs_c": "n.889-2221G>T",
"hgvs_p": null,
"transcript": "ENST00000675742.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3351,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "ATP1A1-AS1",
"gene_hgnc_id": 28262,
"hgvs_c": "n.401-2221G>T",
"hgvs_p": null,
"transcript": "NR_027646.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 562,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP1A1",
"gene_hgnc_id": 799,
"dbsnp": "rs1553192091",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.811403214931488,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.807,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9471,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.26,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.899,
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3,PP5_Moderate",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000295598.10",
"gene_symbol": "ATP1A1",
"hgnc_id": 799,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1798C>A",
"hgvs_p": "p.Pro600Thr"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000608511.6",
"gene_symbol": "ATP1A1-AS1",
"hgnc_id": 28262,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.411-2221G>T",
"hgvs_p": null
}
],
"clinvar_disease": " axonal, type 2DD,Charcot-Marie-Tooth disease type 2A2,Charcot-Marie-tooth disease,not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Charcot-Marie-tooth disease, axonal, type 2DD|not provided|Charcot-Marie-Tooth disease type 2A2",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}