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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-53415155-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=53415155&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 53415155,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000322213.9",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.124A>G",
"hgvs_p": "p.Met42Val",
"transcript": "NM_006306.4",
"protein_id": "NP_006297.2",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 1233,
"cds_start": 124,
"cds_end": null,
"cds_length": 3702,
"cdna_start": 178,
"cdna_end": null,
"cdna_length": 9710,
"mane_select": "ENST00000322213.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.124A>G",
"hgvs_p": "p.Met42Val",
"transcript": "ENST00000322213.9",
"protein_id": "ENSP00000323421.3",
"transcript_support_level": 1,
"aa_start": 42,
"aa_end": null,
"aa_length": 1233,
"cds_start": 124,
"cds_end": null,
"cds_length": 3702,
"cdna_start": 178,
"cdna_end": null,
"cdna_length": 9710,
"mane_select": "NM_006306.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.58A>G",
"hgvs_p": "p.Met20Val",
"transcript": "ENST00000375340.10",
"protein_id": "ENSP00000364489.7",
"transcript_support_level": 1,
"aa_start": 20,
"aa_end": null,
"aa_length": 1211,
"cds_start": 58,
"cds_end": null,
"cds_length": 3636,
"cdna_start": 398,
"cdna_end": null,
"cdna_length": 9930,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.58A>G",
"hgvs_p": "p.Met20Val",
"transcript": "NM_001281463.1",
"protein_id": "NP_001268392.1",
"transcript_support_level": null,
"aa_start": 20,
"aa_end": null,
"aa_length": 1211,
"cds_start": 58,
"cds_end": null,
"cds_length": 3636,
"cdna_start": 398,
"cdna_end": null,
"cdna_length": 9930,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.58A>G",
"hgvs_p": "p.Met20Val",
"transcript": "ENST00000675504.1",
"protein_id": "ENSP00000502524.1",
"transcript_support_level": null,
"aa_start": 20,
"aa_end": null,
"aa_length": 1211,
"cds_start": 58,
"cds_end": null,
"cds_length": 3636,
"cdna_start": 294,
"cdna_end": null,
"cdna_length": 9826,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.58A>G",
"hgvs_p": "p.Met20Val",
"transcript": "ENST00000674590.1",
"protein_id": "ENSP00000502626.1",
"transcript_support_level": null,
"aa_start": 20,
"aa_end": null,
"aa_length": 977,
"cds_start": 58,
"cds_end": null,
"cds_length": 2934,
"cdna_start": 398,
"cdna_end": null,
"cdna_length": 3323,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "n.178A>G",
"hgvs_p": null,
"transcript": "ENST00000675065.1",
"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": 1761,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "n.110-1720A>G",
"hgvs_p": null,
"transcript": "ENST00000463684.1",
"protein_id": "ENSP00000476958.1",
"transcript_support_level": 2,
"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": 880,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"dbsnp": "rs1556891104",
"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": 0.8935786485671997,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.594,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9695,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.6,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.906,
"phylop100way_prediction": "Pathogenic",
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM1",
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000322213.9",
"gene_symbol": "SMC1A",
"hgnc_id": 11111,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,XL",
"hgvs_c": "c.124A>G",
"hgvs_p": "p.Met42Val"
}
],
"clinvar_disease": "Congenital muscular hypertrophy-cerebral syndrome",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:1",
"phenotype_combined": "Congenital muscular hypertrophy-cerebral syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}