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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: 21-46112179-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=46112179&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "21",
"pos": 46112179,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000300527.9",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A2",
"gene_hgnc_id": 2212,
"hgvs_c": "c.316G>A",
"hgvs_p": "p.Glu106Lys",
"transcript": "NM_001849.4",
"protein_id": "NP_001840.3",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 1019,
"cds_start": 316,
"cds_end": null,
"cds_length": 3060,
"cdna_start": 405,
"cdna_end": null,
"cdna_length": 3445,
"mane_select": "ENST00000300527.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A2",
"gene_hgnc_id": 2212,
"hgvs_c": "c.316G>A",
"hgvs_p": "p.Glu106Lys",
"transcript": "ENST00000300527.9",
"protein_id": "ENSP00000300527.4",
"transcript_support_level": 1,
"aa_start": 106,
"aa_end": null,
"aa_length": 1019,
"cds_start": 316,
"cds_end": null,
"cds_length": 3060,
"cdna_start": 405,
"cdna_end": null,
"cdna_length": 3445,
"mane_select": "NM_001849.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A2",
"gene_hgnc_id": 2212,
"hgvs_c": "c.316G>A",
"hgvs_p": "p.Glu106Lys",
"transcript": "NM_058174.3",
"protein_id": "NP_478054.2",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 918,
"cds_start": 316,
"cds_end": null,
"cds_length": 2757,
"cdna_start": 405,
"cdna_end": null,
"cdna_length": 3156,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A2",
"gene_hgnc_id": 2212,
"hgvs_c": "c.316G>A",
"hgvs_p": "p.Glu106Lys",
"transcript": "ENST00000397763.6",
"protein_id": "ENSP00000380870.1",
"transcript_support_level": 5,
"aa_start": 106,
"aa_end": null,
"aa_length": 918,
"cds_start": 316,
"cds_end": null,
"cds_length": 2757,
"cdna_start": 405,
"cdna_end": null,
"cdna_length": 3156,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A2",
"gene_hgnc_id": 2212,
"hgvs_c": "c.316G>A",
"hgvs_p": "p.Glu106Lys",
"transcript": "NM_058175.3",
"protein_id": "NP_478055.2",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 828,
"cds_start": 316,
"cds_end": null,
"cds_length": 2487,
"cdna_start": 405,
"cdna_end": null,
"cdna_length": 3449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A2",
"gene_hgnc_id": 2212,
"hgvs_c": "c.316G>A",
"hgvs_p": "p.Glu106Lys",
"transcript": "ENST00000409416.6",
"protein_id": "ENSP00000387115.1",
"transcript_support_level": 5,
"aa_start": 106,
"aa_end": null,
"aa_length": 828,
"cds_start": 316,
"cds_end": null,
"cds_length": 2487,
"cdna_start": 316,
"cdna_end": null,
"cdna_length": 3367,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A2",
"gene_hgnc_id": 2212,
"hgvs_c": "c.316G>A",
"hgvs_p": "p.Glu106Lys",
"transcript": "ENST00000436769.5",
"protein_id": "ENSP00000390418.1",
"transcript_support_level": 2,
"aa_start": 106,
"aa_end": null,
"aa_length": 179,
"cds_start": 316,
"cds_end": null,
"cds_length": 541,
"cdna_start": 694,
"cdna_end": null,
"cdna_length": 919,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A2",
"gene_hgnc_id": 2212,
"hgvs_c": "n.-239G>A",
"hgvs_p": null,
"transcript": "ENST00000460886.1",
"protein_id": null,
"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": 306,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124905043",
"gene_hgnc_id": null,
"hgvs_c": "n.-148C>T",
"hgvs_p": null,
"transcript": "XR_007067910.1",
"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": 2743,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL6A2",
"gene_hgnc_id": 2212,
"dbsnp": "rs141703710",
"frequency_reference_population": 0.011296454,
"hom_count_reference_population": 128,
"allele_count_reference_population": 18221,
"gnomad_exomes_af": 0.0117597,
"gnomad_genomes_af": 0.00685435,
"gnomad_exomes_ac": 17177,
"gnomad_genomes_ac": 1044,
"gnomad_exomes_homalt": 119,
"gnomad_genomes_homalt": 9,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009793192148208618,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.276,
"revel_prediction": "Benign",
"alphamissense_score": 0.0949,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.479,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000300527.9",
"gene_symbol": "COL6A2",
"hgnc_id": 2212,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.316G>A",
"hgvs_p": "p.Glu106Lys"
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "XR_007067910.1",
"gene_symbol": "LOC124905043",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-148C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Bethlem myopathy 1A,Collagen 6-related myopathy,Myosclerosis,Ullrich congenital muscular dystrophy 1A,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:7",
"phenotype_combined": "not specified|not provided|Collagen 6-related myopathy|Bethlem myopathy 1A|Myosclerosis;Bethlem myopathy 1A;Ullrich congenital muscular dystrophy 1A",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}