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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-78042646-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=78042646&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 78042646,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000341514.11",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.3863A>G",
"hgvs_p": "p.Gln1288Arg",
"transcript": "NM_000052.7",
"protein_id": "NP_000043.4",
"transcript_support_level": null,
"aa_start": 1288,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3863,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 4027,
"cdna_end": null,
"cdna_length": 8492,
"mane_select": "ENST00000341514.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.3863A>G",
"hgvs_p": "p.Gln1288Arg",
"transcript": "ENST00000341514.11",
"protein_id": "ENSP00000345728.6",
"transcript_support_level": 1,
"aa_start": 1288,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3863,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 4027,
"cdna_end": null,
"cdna_length": 8492,
"mane_select": "NM_000052.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.3956A>G",
"hgvs_p": "p.Gln1319Arg",
"transcript": "ENST00000689767.1",
"protein_id": "ENSP00000509406.1",
"transcript_support_level": null,
"aa_start": 1319,
"aa_end": null,
"aa_length": 1531,
"cds_start": 3956,
"cds_end": null,
"cds_length": 4596,
"cdna_start": 4104,
"cdna_end": null,
"cdna_length": 8569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.3893A>G",
"hgvs_p": "p.Gln1298Arg",
"transcript": "ENST00000343533.10",
"protein_id": "ENSP00000343026.6",
"transcript_support_level": 5,
"aa_start": 1298,
"aa_end": null,
"aa_length": 1510,
"cds_start": 3893,
"cds_end": null,
"cds_length": 4533,
"cdna_start": 4083,
"cdna_end": null,
"cdna_length": 8548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.3863A>G",
"hgvs_p": "p.Gln1288Arg",
"transcript": "ENST00000685264.1",
"protein_id": "ENSP00000510136.1",
"transcript_support_level": null,
"aa_start": 1288,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3863,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 4055,
"cdna_end": null,
"cdna_length": 4984,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.3863A>G",
"hgvs_p": "p.Gln1288Arg",
"transcript": "ENST00000686133.1",
"protein_id": "ENSP00000509233.1",
"transcript_support_level": null,
"aa_start": 1288,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3863,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 4034,
"cdna_end": null,
"cdna_length": 5003,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.3863A>G",
"hgvs_p": "p.Gln1288Arg",
"transcript": "ENST00000687086.1",
"protein_id": "ENSP00000509566.1",
"transcript_support_level": null,
"aa_start": 1288,
"aa_end": null,
"aa_length": 1500,
"cds_start": 3863,
"cds_end": null,
"cds_length": 4503,
"cdna_start": 4176,
"cdna_end": null,
"cdna_length": 5092,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.3668A>G",
"hgvs_p": "p.Gln1223Arg",
"transcript": "ENST00000686033.1",
"protein_id": "ENSP00000510693.1",
"transcript_support_level": null,
"aa_start": 1223,
"aa_end": null,
"aa_length": 1435,
"cds_start": 3668,
"cds_end": null,
"cds_length": 4308,
"cdna_start": 3786,
"cdna_end": null,
"cdna_length": 4755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.3629A>G",
"hgvs_p": "p.Gln1210Arg",
"transcript": "NM_001282224.2",
"protein_id": "NP_001269153.1",
"transcript_support_level": null,
"aa_start": 1210,
"aa_end": null,
"aa_length": 1422,
"cds_start": 3629,
"cds_end": null,
"cds_length": 4269,
"cdna_start": 3793,
"cdna_end": null,
"cdna_length": 8258,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.3629A>G",
"hgvs_p": "p.Gln1210Arg",
"transcript": "ENST00000686543.1",
"protein_id": "ENSP00000509477.1",
"transcript_support_level": null,
"aa_start": 1210,
"aa_end": null,
"aa_length": 1422,
"cds_start": 3629,
"cds_end": null,
"cds_length": 4269,
"cdna_start": 3747,
"cdna_end": null,
"cdna_length": 4716,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.3629A>G",
"hgvs_p": "p.Gln1210Arg",
"transcript": "ENST00000692908.1",
"protein_id": "ENSP00000508627.1",
"transcript_support_level": null,
"aa_start": 1210,
"aa_end": null,
"aa_length": 1422,
"cds_start": 3629,
"cds_end": null,
"cds_length": 4269,
"cdna_start": 3939,
"cdna_end": null,
"cdna_length": 4908,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.1127A>G",
"hgvs_p": "p.Gln376Arg",
"transcript": "ENST00000685033.1",
"protein_id": "ENSP00000509269.1",
"transcript_support_level": null,
"aa_start": 376,
"aa_end": null,
"aa_length": 588,
"cds_start": 1127,
"cds_end": null,
"cds_length": 1767,
"cdna_start": 1127,
"cdna_end": null,
"cdna_length": 5592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.2280A>G",
"hgvs_p": null,
"transcript": "ENST00000682475.1",
"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": 6274,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.2894A>G",
"hgvs_p": null,
"transcript": "ENST00000686255.1",
"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": 7359,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.1905A>G",
"hgvs_p": null,
"transcript": "ENST00000689514.1",
"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": 2388,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.1036A>G",
"hgvs_p": null,
"transcript": "NR_104109.2",
"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": 5501,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.-19-67221A>G",
"hgvs_p": null,
"transcript": "ENST00000644362.1",
"protein_id": "ENSP00000496140.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 389,
"cds_start": -4,
"cds_end": null,
"cds_length": 1170,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2405,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.*3777A>G",
"hgvs_p": null,
"transcript": "ENST00000645094.1",
"protein_id": "ENSP00000493605.1",
"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": 4019,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"dbsnp": "rs375788705",
"frequency_reference_population": 0.000050393315,
"hom_count_reference_population": 24,
"allele_count_reference_population": 61,
"gnomad_exomes_af": 0.0000519024,
"gnomad_genomes_af": 0.0000356309,
"gnomad_exomes_ac": 57,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.378318727016449,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.719,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1495,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.28,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.224,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.07,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BP6,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000341514.11",
"gene_symbol": "ATP7A",
"hgnc_id": 869,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.3863A>G",
"hgvs_p": "p.Gln1288Arg"
},
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000644362.1",
"gene_symbol": "PGK1",
"hgnc_id": 8896,
"effects": [
"intron_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.-19-67221A>G",
"hgvs_p": null
}
],
"clinvar_disease": " X-linked,Cutis laxa,Inborn genetic diseases,Menkes kinky-hair syndrome,X-linked distal spinal muscular atrophy type 3,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:3",
"phenotype_combined": "not provided|Menkes kinky-hair syndrome;X-linked distal spinal muscular atrophy type 3;Cutis laxa, X-linked|Menkes kinky-hair syndrome|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}