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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: 1-160129045-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=160129045&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 160129045,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000702.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.1282C>T",
"hgvs_p": "p.Arg428Cys",
"transcript": "NM_000702.4",
"protein_id": "NP_000693.1",
"transcript_support_level": null,
"aa_start": 428,
"aa_end": null,
"aa_length": 1020,
"cds_start": 1282,
"cds_end": null,
"cds_length": 3063,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000361216.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000702.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.1282C>T",
"hgvs_p": "p.Arg428Cys",
"transcript": "ENST00000361216.8",
"protein_id": "ENSP00000354490.3",
"transcript_support_level": 1,
"aa_start": 428,
"aa_end": null,
"aa_length": 1020,
"cds_start": 1282,
"cds_end": null,
"cds_length": 3063,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000702.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361216.8"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.1282C>T",
"hgvs_p": "p.Arg428Cys",
"transcript": "ENST00000857225.1",
"protein_id": "ENSP00000527284.1",
"transcript_support_level": null,
"aa_start": 428,
"aa_end": null,
"aa_length": 1028,
"cds_start": 1282,
"cds_end": null,
"cds_length": 3087,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857225.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.1282C>T",
"hgvs_p": "p.Arg428Cys",
"transcript": "ENST00000969831.1",
"protein_id": "ENSP00000639890.1",
"transcript_support_level": null,
"aa_start": 428,
"aa_end": null,
"aa_length": 1019,
"cds_start": 1282,
"cds_end": null,
"cds_length": 3060,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969831.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.1273C>T",
"hgvs_p": "p.Arg425Cys",
"transcript": "ENST00000969832.1",
"protein_id": "ENSP00000639891.1",
"transcript_support_level": null,
"aa_start": 425,
"aa_end": null,
"aa_length": 1017,
"cds_start": 1273,
"cds_end": null,
"cds_length": 3054,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969832.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.1252C>T",
"hgvs_p": "p.Arg418Cys",
"transcript": "ENST00000857224.1",
"protein_id": "ENSP00000527283.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 1010,
"cds_start": 1252,
"cds_end": null,
"cds_length": 3033,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857224.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.1282C>T",
"hgvs_p": "p.Arg428Cys",
"transcript": "ENST00000392233.7",
"protein_id": "ENSP00000376066.3",
"transcript_support_level": 5,
"aa_start": 428,
"aa_end": null,
"aa_length": 1009,
"cds_start": 1282,
"cds_end": null,
"cds_length": 3030,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392233.7"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.1219C>T",
"hgvs_p": "p.Arg407Cys",
"transcript": "ENST00000857223.1",
"protein_id": "ENSP00000527282.1",
"transcript_support_level": null,
"aa_start": 407,
"aa_end": null,
"aa_length": 999,
"cds_start": 1219,
"cds_end": null,
"cds_length": 3000,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857223.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.1078C>T",
"hgvs_p": "p.Arg360Cys",
"transcript": "ENST00000969833.1",
"protein_id": "ENSP00000639892.1",
"transcript_support_level": null,
"aa_start": 360,
"aa_end": null,
"aa_length": 952,
"cds_start": 1078,
"cds_end": null,
"cds_length": 2859,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969833.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.Arg138Cys",
"transcript": "ENST00000447527.1",
"protein_id": "ENSP00000411705.1",
"transcript_support_level": 2,
"aa_start": 138,
"aa_end": null,
"aa_length": 713,
"cds_start": 412,
"cds_end": null,
"cds_length": 2142,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000447527.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "c.391C>T",
"hgvs_p": "p.Arg131Cys",
"transcript": "XM_047421286.1",
"protein_id": "XP_047277242.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 723,
"cds_start": 391,
"cds_end": null,
"cds_length": 2172,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047421286.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"hgvs_c": "n.1385C>T",
"hgvs_p": null,
"transcript": "ENST00000472488.5",
"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": "ENST00000472488.5"
}
],
"gene_symbol": "ATP1A2",
"gene_hgnc_id": 800,
"dbsnp": "rs779985796",
"frequency_reference_population": 0.0000041088124,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000410881,
"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": 0.9149688482284546,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.85,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9398,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.34,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.73,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PP2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000702.4",
"gene_symbol": "ATP1A2",
"hgnc_id": 800,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1282C>T",
"hgvs_p": "p.Arg428Cys"
}
],
"clinvar_disease": " 2, familial hemiplegic,Alternating hemiplegia of childhood 1,Familial hemiplegic migraine,Inborn genetic diseases,Migraine,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"phenotype_combined": "not provided|Alternating hemiplegia of childhood 1;Migraine, familial hemiplegic, 2|Familial hemiplegic migraine|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}