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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: 1-116387415-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=116387415&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PM5",
"PP3_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ATP1A1",
"hgnc_id": 799,
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"inheritance_mode": "AD",
"pathogenic_score": 8,
"score": 8,
"transcript": "NM_000701.8",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ATP1A1-AS1",
"hgnc_id": 28262,
"hgvs_c": "n.386-7370A>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 6,
"score": 6,
"transcript": "ENST00000675607.1",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Strong",
"acmg_score": 8,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.9987,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.53,
"chr": "1",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9471258521080017,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1023,
"aa_ref": "L",
"aa_start": 104,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3670,
"cdna_start": 579,
"cds_end": null,
"cds_length": 3072,
"cds_start": 311,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_000701.8",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000295598.10",
"protein_coding": true,
"protein_id": "NP_000692.2",
"strand": true,
"transcript": "NM_000701.8",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1023,
"aa_ref": "L",
"aa_start": 104,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3670,
"cdna_start": 579,
"cds_end": null,
"cds_length": 3072,
"cds_start": 311,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000295598.10",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000701.8",
"protein_coding": true,
"protein_id": "ENSP00000295598.5",
"strand": true,
"transcript": "ENST00000295598.10",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1076,
"aa_ref": "L",
"aa_start": 104,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3829,
"cdna_start": 579,
"cds_end": null,
"cds_length": 3231,
"cds_start": 311,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000897942.1",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568001.1",
"strand": true,
"transcript": "ENST00000897942.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1036,
"aa_ref": "L",
"aa_start": 104,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3654,
"cdna_start": 527,
"cds_end": null,
"cds_length": 3111,
"cds_start": 311,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000945201.1",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000615260.1",
"strand": true,
"transcript": "ENST00000945201.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1023,
"aa_ref": "L",
"aa_start": 104,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3765,
"cdna_start": 674,
"cds_end": null,
"cds_length": 3072,
"cds_start": 311,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001160233.2",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001153705.1",
"strand": true,
"transcript": "NM_001160233.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1023,
"aa_ref": "L",
"aa_start": 104,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3763,
"cdna_start": 674,
"cds_end": null,
"cds_length": 3072,
"cds_start": 311,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000537345.5",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000445306.1",
"strand": true,
"transcript": "ENST00000537345.5",
"transcript_support_level": 2
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1023,
"aa_ref": "L",
"aa_start": 104,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3627,
"cdna_start": 536,
"cds_end": null,
"cds_length": 3072,
"cds_start": 311,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000897938.1",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000567997.1",
"strand": true,
"transcript": "ENST00000897938.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1022,
"aa_ref": "L",
"aa_start": 104,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3667,
"cdna_start": 579,
"cds_end": null,
"cds_length": 3069,
"cds_start": 311,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000897941.1",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568000.1",
"strand": true,
"transcript": "ENST00000897941.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1019,
"aa_ref": "L",
"aa_start": 104,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3699,
"cdna_start": 620,
"cds_end": null,
"cds_length": 3060,
"cds_start": 311,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000897939.1",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000567998.1",
"strand": true,
"transcript": "ENST00000897939.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1019,
"aa_ref": "L",
"aa_start": 104,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3655,
"cdna_start": 579,
"cds_end": null,
"cds_length": 3060,
"cds_start": 311,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000897944.1",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568003.1",
"strand": true,
"transcript": "ENST00000897944.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 992,
"aa_ref": "L",
"aa_start": 73,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3574,
"cdna_start": 483,
"cds_end": null,
"cds_length": 2979,
"cds_start": 218,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001160234.2",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.218T>C",
"hgvs_p": "p.Leu73Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001153706.1",
"strand": true,
"transcript": "NM_001160234.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 992,
"aa_ref": "L",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3572,
"cdna_start": 483,
"cds_end": null,
"cds_length": 2979,
"cds_start": 218,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000369496.8",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.218T>C",
"hgvs_p": "p.Leu73Pro",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000358508.4",
"strand": true,
"transcript": "ENST00000369496.8",
"transcript_support_level": 2
},
{
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"aa_length": 985,
"aa_ref": "L",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3553,
"cdna_start": 579,
"cds_end": null,
"cds_length": 2958,
"cds_start": 311,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000897943.1",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568002.1",
"strand": true,
"transcript": "ENST00000897943.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
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"aa_length": 978,
"aa_ref": "L",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3528,
"cdna_start": 579,
"cds_end": null,
"cds_length": 2937,
"cds_start": 311,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000945199.1",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000615258.1",
"strand": true,
"transcript": "ENST00000945199.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 867,
"aa_ref": "L",
"aa_start": 104,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3207,
"cdna_start": 584,
"cds_end": null,
"cds_length": 2604,
"cds_start": 311,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000897940.1",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.311T>C",
"hgvs_p": "p.Leu104Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000567999.1",
"strand": true,
"transcript": "ENST00000897940.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 143,
"aa_ref": "L",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 698,
"cdna_start": 482,
"cds_end": null,
"cds_length": 434,
"cds_start": 218,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000369494.5",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.218T>C",
"hgvs_p": "p.Leu73Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000358506.1",
"strand": true,
"transcript": "ENST00000369494.5",
"transcript_support_level": 3
},
{
"aa_alt": "P",
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"aa_length": 105,
"aa_ref": "L",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 654,
"cdna_start": 553,
"cds_end": null,
"cds_length": 319,
"cds_start": 218,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000418797.5",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.218T>C",
"hgvs_p": "p.Leu73Pro",
"intron_rank": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "ENSP00000400124.1",
"strand": true,
"transcript": "ENST00000418797.5",
"transcript_support_level": 3
},
{
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"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3450,
"cdna_start": null,
"cds_end": null,
"cds_length": 2868,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000945200.1",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.184-716T>C",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000615259.1",
"strand": true,
"transcript": "ENST00000945200.1",
"transcript_support_level": null
},
{
"aa_alt": null,
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"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2013,
"cdna_start": null,
"cds_end": null,
"cds_length": 1419,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000897945.1",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "c.183+2573T>C",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568004.1",
"strand": true,
"transcript": "ENST00000897945.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 584,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000463382.1",
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"hgvs_c": "n.113T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000463382.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1014,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
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"feature": "ENST00000675607.1",
"gene_hgnc_id": 28262,
"gene_symbol": "ATP1A1-AS1",
"hgvs_c": "n.386-7370A>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000675607.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs11540945",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 799,
"gene_symbol": "ATP1A1",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"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": "Uncertain significance",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 8.017,
"pos": 116387415,
"ref": "T",
"revel_prediction": "Pathogenic",
"revel_score": 0.977,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000701.8"
}
]
}