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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: 6-75152156-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=75152156&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 75152156,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000322507.13",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.3810G>A",
"hgvs_p": "p.Pro1270Pro",
"transcript": "NM_004370.6",
"protein_id": "NP_004361.3",
"transcript_support_level": null,
"aa_start": 1270,
"aa_end": null,
"aa_length": 3063,
"cds_start": 3810,
"cds_end": null,
"cds_length": 9192,
"cdna_start": 4122,
"cdna_end": null,
"cdna_length": 11725,
"mane_select": "ENST00000322507.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.3810G>A",
"hgvs_p": "p.Pro1270Pro",
"transcript": "ENST00000322507.13",
"protein_id": "ENSP00000325146.8",
"transcript_support_level": 1,
"aa_start": 1270,
"aa_end": null,
"aa_length": 3063,
"cds_start": 3810,
"cds_end": null,
"cds_length": 9192,
"cdna_start": 4122,
"cdna_end": null,
"cdna_length": 11725,
"mane_select": "NM_004370.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.318G>A",
"hgvs_p": "p.Pro106Pro",
"transcript": "ENST00000345356.10",
"protein_id": "ENSP00000305147.9",
"transcript_support_level": 1,
"aa_start": 106,
"aa_end": null,
"aa_length": 1899,
"cds_start": 318,
"cds_end": null,
"cds_length": 5700,
"cdna_start": 428,
"cdna_end": null,
"cdna_length": 5886,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.3810G>A",
"hgvs_p": "p.Pro1270Pro",
"transcript": "NM_001424113.1",
"protein_id": "NP_001411042.1",
"transcript_support_level": null,
"aa_start": 1270,
"aa_end": null,
"aa_length": 3118,
"cds_start": 3810,
"cds_end": null,
"cds_length": 9357,
"cdna_start": 4122,
"cdna_end": null,
"cdna_length": 10533,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.3810G>A",
"hgvs_p": "p.Pro1270Pro",
"transcript": "ENST00000483888.6",
"protein_id": "ENSP00000421216.1",
"transcript_support_level": 5,
"aa_start": 1270,
"aa_end": null,
"aa_length": 3062,
"cds_start": 3810,
"cds_end": null,
"cds_length": 9189,
"cdna_start": 3891,
"cdna_end": null,
"cdna_length": 9637,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.3810G>A",
"hgvs_p": "p.Pro1270Pro",
"transcript": "NM_001424114.1",
"protein_id": "NP_001411043.1",
"transcript_support_level": null,
"aa_start": 1270,
"aa_end": null,
"aa_length": 3056,
"cds_start": 3810,
"cds_end": null,
"cds_length": 9171,
"cdna_start": 4122,
"cdna_end": null,
"cdna_length": 11704,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.3810G>A",
"hgvs_p": "p.Pro1270Pro",
"transcript": "ENST00000416123.6",
"protein_id": "ENSP00000412864.2",
"transcript_support_level": 5,
"aa_start": 1270,
"aa_end": null,
"aa_length": 2987,
"cds_start": 3810,
"cds_end": null,
"cds_length": 8964,
"cdna_start": 3810,
"cdna_end": null,
"cdna_length": 8964,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.3537G>A",
"hgvs_p": "p.Pro1179Pro",
"transcript": "NM_001424115.1",
"protein_id": "NP_001411044.1",
"transcript_support_level": null,
"aa_start": 1179,
"aa_end": null,
"aa_length": 2972,
"cds_start": 3537,
"cds_end": null,
"cds_length": 8919,
"cdna_start": 3849,
"cdna_end": null,
"cdna_length": 11452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.318G>A",
"hgvs_p": "p.Pro106Pro",
"transcript": "NM_001424116.1",
"protein_id": "NP_001411045.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 1954,
"cds_start": 318,
"cds_end": null,
"cds_length": 5865,
"cdna_start": 630,
"cdna_end": null,
"cdna_length": 7041,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.318G>A",
"hgvs_p": "p.Pro106Pro",
"transcript": "NM_080645.3",
"protein_id": "NP_542376.2",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 1899,
"cds_start": 318,
"cds_end": null,
"cds_length": 5700,
"cdna_start": 630,
"cdna_end": null,
"cdna_length": 8233,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.33G>A",
"hgvs_p": "p.Pro11Pro",
"transcript": "ENST00000419671.1",
"protein_id": "ENSP00000393217.1",
"transcript_support_level": 5,
"aa_start": 11,
"aa_end": null,
"aa_length": 636,
"cds_start": 33,
"cds_end": null,
"cds_length": 1913,
"cdna_start": 34,
"cdna_end": null,
"cdna_length": 1914,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.3810G>A",
"hgvs_p": "p.Pro1270Pro",
"transcript": "XM_047418184.1",
"protein_id": "XP_047274140.1",
"transcript_support_level": null,
"aa_start": 1270,
"aa_end": null,
"aa_length": 3118,
"cds_start": 3810,
"cds_end": null,
"cds_length": 9357,
"cdna_start": 4172,
"cdna_end": null,
"cdna_length": 10583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.3774G>A",
"hgvs_p": "p.Pro1258Pro",
"transcript": "XM_017010252.3",
"protein_id": "XP_016865741.1",
"transcript_support_level": null,
"aa_start": 1258,
"aa_end": null,
"aa_length": 3106,
"cds_start": 3774,
"cds_end": null,
"cds_length": 9321,
"cdna_start": 4369,
"cdna_end": null,
"cdna_length": 10780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.3537G>A",
"hgvs_p": "p.Pro1179Pro",
"transcript": "XM_011535435.2",
"protein_id": "XP_011533737.1",
"transcript_support_level": null,
"aa_start": 1179,
"aa_end": null,
"aa_length": 3027,
"cds_start": 3537,
"cds_end": null,
"cds_length": 9084,
"cdna_start": 3849,
"cdna_end": null,
"cdna_length": 10260,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.318G>A",
"hgvs_p": "p.Pro106Pro",
"transcript": "XM_047418186.1",
"protein_id": "XP_047274142.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 1899,
"cds_start": 318,
"cds_end": null,
"cds_length": 5700,
"cdna_start": 680,
"cdna_end": null,
"cdna_length": 8283,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"dbsnp": "rs370675782",
"frequency_reference_population": 0.000045857232,
"hom_count_reference_population": 1,
"allele_count_reference_population": 74,
"gnomad_exomes_af": 0.0000485781,
"gnomad_genomes_af": 0.0000197187,
"gnomad_exomes_ac": 71,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.061000000685453415,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.061,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.915,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BP7,BS1",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BP7",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000322507.13",
"gene_symbol": "COL12A1",
"hgnc_id": 2188,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3810G>A",
"hgvs_p": "p.Pro1270Pro"
}
],
"clinvar_disease": "Bethlem myopathy 2,Ullrich congenital muscular dystrophy 2",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Ullrich congenital muscular dystrophy 2;Bethlem myopathy 2",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}