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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: 2-237344760-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=237344760&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 237344760,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000295550.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.7258C>T",
"hgvs_p": "p.Arg2420Trp",
"transcript": "NM_004369.4",
"protein_id": "NP_004360.2",
"transcript_support_level": null,
"aa_start": 2420,
"aa_end": null,
"aa_length": 3177,
"cds_start": 7258,
"cds_end": null,
"cds_length": 9534,
"cdna_start": 7500,
"cdna_end": null,
"cdna_length": 10532,
"mane_select": "ENST00000295550.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.7258C>T",
"hgvs_p": "p.Arg2420Trp",
"transcript": "ENST00000295550.9",
"protein_id": "ENSP00000295550.4",
"transcript_support_level": 1,
"aa_start": 2420,
"aa_end": null,
"aa_length": 3177,
"cds_start": 7258,
"cds_end": null,
"cds_length": 9534,
"cdna_start": 7500,
"cdna_end": null,
"cdna_length": 10532,
"mane_select": "NM_004369.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.5437C>T",
"hgvs_p": "p.Arg1813Trp",
"transcript": "ENST00000472056.5",
"protein_id": "ENSP00000418285.1",
"transcript_support_level": 1,
"aa_start": 1813,
"aa_end": null,
"aa_length": 2570,
"cds_start": 5437,
"cds_end": null,
"cds_length": 7713,
"cdna_start": 5663,
"cdna_end": null,
"cdna_length": 8628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.6640C>T",
"hgvs_p": "p.Arg2214Trp",
"transcript": "NM_057167.4",
"protein_id": "NP_476508.2",
"transcript_support_level": null,
"aa_start": 2214,
"aa_end": null,
"aa_length": 2971,
"cds_start": 6640,
"cds_end": null,
"cds_length": 8916,
"cdna_start": 6882,
"cdna_end": null,
"cdna_length": 9914,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.6640C>T",
"hgvs_p": "p.Arg2214Trp",
"transcript": "ENST00000353578.9",
"protein_id": "ENSP00000315873.4",
"transcript_support_level": 5,
"aa_start": 2214,
"aa_end": null,
"aa_length": 2971,
"cds_start": 6640,
"cds_end": null,
"cds_length": 8916,
"cdna_start": 6890,
"cdna_end": null,
"cdna_length": 9636,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.5437C>T",
"hgvs_p": "p.Arg1813Trp",
"transcript": "NM_057166.5",
"protein_id": "NP_476507.3",
"transcript_support_level": null,
"aa_start": 1813,
"aa_end": null,
"aa_length": 2570,
"cds_start": 5437,
"cds_end": null,
"cds_length": 7713,
"cdna_start": 5679,
"cdna_end": null,
"cdna_length": 8711,
"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": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "n.1512C>T",
"hgvs_p": null,
"transcript": "ENST00000491769.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 6731,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.-99C>T",
"hgvs_p": null,
"transcript": "ENST00000347401.8",
"protein_id": "ENSP00000315609.5",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 637,
"cds_start": -4,
"cds_end": null,
"cds_length": 1914,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2670,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"dbsnp": "rs150165484",
"frequency_reference_population": 0.00092416245,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1480,
"gnomad_exomes_af": 0.000926734,
"gnomad_genomes_af": 0.000899694,
"gnomad_exomes_ac": 1343,
"gnomad_genomes_ac": 137,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.056619077920913696,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.55,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1243,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.04,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 1.945,
"phylop100way_prediction": "Benign",
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BS1_Supporting",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS1_Supporting"
],
"verdict": "Likely_benign",
"transcript": "ENST00000295550.9",
"gene_symbol": "COL6A3",
"hgnc_id": 2213,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "c.7258C>T",
"hgvs_p": "p.Arg2420Trp"
}
],
"clinvar_disease": "Bethlem myopathy 1A,Collagen 6-related myopathy,Tip-toe gait,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:4 LB:2 B:1",
"phenotype_combined": "Collagen 6-related myopathy|Bethlem myopathy 1A|Tip-toe gait|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}