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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: X-78015836-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=78015836&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP6_Very_Strong",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ATP7A",
"hgnc_id": 869,
"hgvs_c": "c.2581C>T",
"hgvs_p": "p.Arg861Cys",
"inheritance_mode": "XL,AD",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_000052.7",
"verdict": "Benign"
},
{
"benign_score": 12,
"criteria": [
"BP6_Very_Strong",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "PGK1",
"hgnc_id": 8896,
"hgvs_c": "c.-19-94031C>T",
"hgvs_p": null,
"inheritance_mode": "XL",
"pathogenic_score": 0,
"score": -12,
"transcript": "ENST00000644362.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Very_Strong,BS2",
"acmg_score": -12,
"allele_count_reference_population": 33,
"alphamissense_prediction": null,
"alphamissense_score": 0.098,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.48,
"chr": "X",
"clinvar_classification": "Likely benign",
"clinvar_disease": " X-linked,Cutis laxa,Menkes kinky-hair syndrome,X-linked distal spinal muscular atrophy type 3,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5527255535125732,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1500,
"aa_ref": "R",
"aa_start": 861,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8492,
"cdna_start": 2745,
"cds_end": null,
"cds_length": 4503,
"cds_start": 2581,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_000052.7",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "c.2581C>T",
"hgvs_p": "p.Arg861Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000341514.11",
"protein_coding": true,
"protein_id": "NP_000043.4",
"strand": true,
"transcript": "NM_000052.7",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1500,
"aa_ref": "R",
"aa_start": 861,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8492,
"cdna_start": 2745,
"cds_end": null,
"cds_length": 4503,
"cds_start": 2581,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000341514.11",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "c.2581C>T",
"hgvs_p": "p.Arg861Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000052.7",
"protein_coding": true,
"protein_id": "ENSP00000345728.6",
"strand": true,
"transcript": "ENST00000341514.11",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1531,
"aa_ref": "R",
"aa_start": 892,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8569,
"cdna_start": 2822,
"cds_end": null,
"cds_length": 4596,
"cds_start": 2674,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000689767.1",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "c.2674C>T",
"hgvs_p": "p.Arg892Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509406.1",
"strand": true,
"transcript": "ENST00000689767.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1510,
"aa_ref": "R",
"aa_start": 871,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8548,
"cdna_start": 2801,
"cds_end": null,
"cds_length": 4533,
"cds_start": 2611,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000343533.10",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "c.2611C>T",
"hgvs_p": "p.Arg871Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000343026.6",
"strand": true,
"transcript": "ENST00000343533.10",
"transcript_support_level": 5
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1500,
"aa_ref": "R",
"aa_start": 861,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4984,
"cdna_start": 2773,
"cds_end": null,
"cds_length": 4503,
"cds_start": 2581,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000685264.1",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "c.2581C>T",
"hgvs_p": "p.Arg861Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000510136.1",
"strand": true,
"transcript": "ENST00000685264.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1500,
"aa_ref": "R",
"aa_start": 861,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5003,
"cdna_start": 2752,
"cds_end": null,
"cds_length": 4503,
"cds_start": 2581,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000686133.1",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "c.2581C>T",
"hgvs_p": "p.Arg861Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509233.1",
"strand": true,
"transcript": "ENST00000686133.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1500,
"aa_ref": "R",
"aa_start": 861,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5092,
"cdna_start": 2894,
"cds_end": null,
"cds_length": 4503,
"cds_start": 2581,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000687086.1",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "c.2581C>T",
"hgvs_p": "p.Arg861Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509566.1",
"strand": true,
"transcript": "ENST00000687086.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1435,
"aa_ref": "R",
"aa_start": 861,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4755,
"cdna_start": 2699,
"cds_end": null,
"cds_length": 4308,
"cds_start": 2581,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000686033.1",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "c.2581C>T",
"hgvs_p": "p.Arg861Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000510693.1",
"strand": true,
"transcript": "ENST00000686033.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1422,
"aa_ref": "R",
"aa_start": 783,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8258,
"cdna_start": 2511,
"cds_end": null,
"cds_length": 4269,
"cds_start": 2347,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001282224.2",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "c.2347C>T",
"hgvs_p": "p.Arg783Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001269153.1",
"strand": true,
"transcript": "NM_001282224.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1422,
"aa_ref": "R",
"aa_start": 783,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4716,
"cdna_start": 2465,
"cds_end": null,
"cds_length": 4269,
"cds_start": 2347,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000686543.1",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "c.2347C>T",
"hgvs_p": "p.Arg783Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509477.1",
"strand": true,
"transcript": "ENST00000686543.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1422,
"aa_ref": "R",
"aa_start": 783,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4908,
"cdna_start": 2657,
"cds_end": null,
"cds_length": 4269,
"cds_start": 2347,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000692908.1",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "c.2347C>T",
"hgvs_p": "p.Arg783Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000508627.1",
"strand": true,
"transcript": "ENST00000692908.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 971,
"aa_ref": "R",
"aa_start": 861,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3250,
"cdna_start": 2915,
"cds_end": null,
"cds_length": 2916,
"cds_start": 2581,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000689530.1",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "c.2581C>T",
"hgvs_p": "p.Arg861Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509707.1",
"strand": true,
"transcript": "ENST00000689530.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 929,
"aa_ref": "R",
"aa_start": 861,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3050,
"cdna_start": 2743,
"cds_end": null,
"cds_length": 2790,
"cds_start": 2581,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000686688.1",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "c.2581C>T",
"hgvs_p": "p.Arg861Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509416.1",
"strand": true,
"transcript": "ENST00000686688.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 929,
"aa_ref": "R",
"aa_start": 861,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3000,
"cdna_start": 2697,
"cds_end": null,
"cds_length": 2790,
"cds_start": 2581,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000693398.1",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "c.2581C>T",
"hgvs_p": "p.Arg861Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000510089.1",
"strand": true,
"transcript": "ENST00000693398.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 588,
"aa_ref": "R",
"aa_start": 59,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5592,
"cdna_start": 175,
"cds_end": null,
"cds_length": 1767,
"cds_start": 175,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000685033.1",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "c.175C>T",
"hgvs_p": "p.Arg59Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509269.1",
"strand": true,
"transcript": "ENST00000685033.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 389,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2405,
"cdna_start": null,
"cds_end": null,
"cds_length": 1170,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000644362.1",
"gene_hgnc_id": 8896,
"gene_symbol": "PGK1",
"hgvs_c": "c.-19-94031C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000496140.1",
"strand": true,
"transcript": "ENST00000644362.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4019,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 21,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000645094.1",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "n.*2495C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000493605.1",
"strand": true,
"transcript": "ENST00000645094.1",
"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": 6274,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000682475.1",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "n.998C>T",
"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": "ENST00000682475.1",
"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": 7359,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 15,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000686255.1",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "n.1612C>T",
"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": "ENST00000686255.1",
"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": 2388,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000689514.1",
"gene_hgnc_id": 869,
"gene_symbol": "ATP7A",
"hgvs_c": "n.623C>T",
"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": "ENST00000689514.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
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{
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],
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]
}