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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-78043359-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=78043359&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 78043359,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_000052.7",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.4048A>G",
"hgvs_p": "p.Lys1350Glu",
"transcript": "NM_000052.7",
"protein_id": "NP_000043.4",
"transcript_support_level": null,
"aa_start": 1350,
"aa_end": null,
"aa_length": 1500,
"cds_start": 4048,
"cds_end": null,
"cds_length": 4503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000341514.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000052.7"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.4048A>G",
"hgvs_p": "p.Lys1350Glu",
"transcript": "ENST00000341514.11",
"protein_id": "ENSP00000345728.6",
"transcript_support_level": 1,
"aa_start": 1350,
"aa_end": null,
"aa_length": 1500,
"cds_start": 4048,
"cds_end": null,
"cds_length": 4503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000052.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000341514.11"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.4141A>G",
"hgvs_p": "p.Lys1381Glu",
"transcript": "ENST00000689767.1",
"protein_id": "ENSP00000509406.1",
"transcript_support_level": null,
"aa_start": 1381,
"aa_end": null,
"aa_length": 1531,
"cds_start": 4141,
"cds_end": null,
"cds_length": 4596,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000689767.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.4078A>G",
"hgvs_p": "p.Lys1360Glu",
"transcript": "ENST00000343533.10",
"protein_id": "ENSP00000343026.6",
"transcript_support_level": 5,
"aa_start": 1360,
"aa_end": null,
"aa_length": 1510,
"cds_start": 4078,
"cds_end": null,
"cds_length": 4533,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000343533.10"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.4048A>G",
"hgvs_p": "p.Lys1350Glu",
"transcript": "ENST00000685264.1",
"protein_id": "ENSP00000510136.1",
"transcript_support_level": null,
"aa_start": 1350,
"aa_end": null,
"aa_length": 1500,
"cds_start": 4048,
"cds_end": null,
"cds_length": 4503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000685264.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.4048A>G",
"hgvs_p": "p.Lys1350Glu",
"transcript": "ENST00000686133.1",
"protein_id": "ENSP00000509233.1",
"transcript_support_level": null,
"aa_start": 1350,
"aa_end": null,
"aa_length": 1500,
"cds_start": 4048,
"cds_end": null,
"cds_length": 4503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000686133.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.4048A>G",
"hgvs_p": "p.Lys1350Glu",
"transcript": "ENST00000687086.1",
"protein_id": "ENSP00000509566.1",
"transcript_support_level": null,
"aa_start": 1350,
"aa_end": null,
"aa_length": 1500,
"cds_start": 4048,
"cds_end": null,
"cds_length": 4503,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000687086.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.3853A>G",
"hgvs_p": "p.Lys1285Glu",
"transcript": "ENST00000686033.1",
"protein_id": "ENSP00000510693.1",
"transcript_support_level": null,
"aa_start": 1285,
"aa_end": null,
"aa_length": 1435,
"cds_start": 3853,
"cds_end": null,
"cds_length": 4308,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000686033.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.3814A>G",
"hgvs_p": "p.Lys1272Glu",
"transcript": "NM_001282224.2",
"protein_id": "NP_001269153.1",
"transcript_support_level": null,
"aa_start": 1272,
"aa_end": null,
"aa_length": 1422,
"cds_start": 3814,
"cds_end": null,
"cds_length": 4269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001282224.2"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.3814A>G",
"hgvs_p": "p.Lys1272Glu",
"transcript": "ENST00000686543.1",
"protein_id": "ENSP00000509477.1",
"transcript_support_level": null,
"aa_start": 1272,
"aa_end": null,
"aa_length": 1422,
"cds_start": 3814,
"cds_end": null,
"cds_length": 4269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000686543.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.3814A>G",
"hgvs_p": "p.Lys1272Glu",
"transcript": "ENST00000692908.1",
"protein_id": "ENSP00000508627.1",
"transcript_support_level": null,
"aa_start": 1272,
"aa_end": null,
"aa_length": 1422,
"cds_start": 3814,
"cds_end": null,
"cds_length": 4269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000692908.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "c.1312A>G",
"hgvs_p": "p.Lys438Glu",
"transcript": "ENST00000685033.1",
"protein_id": "ENSP00000509269.1",
"transcript_support_level": null,
"aa_start": 438,
"aa_end": null,
"aa_length": 588,
"cds_start": 1312,
"cds_end": null,
"cds_length": 1767,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000685033.1"
},
{
"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.-19-66508A>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": null,
"cds_end": null,
"cds_length": 1170,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000644362.1"
},
{
"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": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.2465A>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": 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": "ENST00000682475.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.3079A>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": 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": "ENST00000686255.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.2090A>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": 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": "ENST00000689514.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"hgvs_c": "n.1221A>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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_104109.2"
}
],
"gene_symbol": "ATP7A",
"gene_hgnc_id": 869,
"dbsnp": "rs4826245",
"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": 0.6694408059120178,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": 0.2804,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.845,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP6_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP6_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000052.7",
"gene_symbol": "ATP7A",
"hgnc_id": 869,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.4048A>G",
"hgvs_p": "p.Lys1350Glu"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP6_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000644362.1",
"gene_symbol": "PGK1",
"hgnc_id": 8896,
"effects": [
"intron_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.-19-66508A>G",
"hgvs_p": null
}
],
"clinvar_disease": " X-linked,Cutis laxa,Menkes kinky-hair syndrome,X-linked distal spinal muscular atrophy type 3",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "Menkes kinky-hair syndrome;Cutis laxa, X-linked;X-linked distal spinal muscular atrophy type 3",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}