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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: 6-75165525-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=75165525&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 75165525,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000322507.13",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.2965G>A",
"hgvs_p": "p.Gly989Arg",
"transcript": "NM_004370.6",
"protein_id": "NP_004361.3",
"transcript_support_level": null,
"aa_start": 989,
"aa_end": null,
"aa_length": 3063,
"cds_start": 2965,
"cds_end": null,
"cds_length": 9192,
"cdna_start": 3277,
"cdna_end": null,
"cdna_length": 11725,
"mane_select": "ENST00000322507.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.2965G>A",
"hgvs_p": "p.Gly989Arg",
"transcript": "ENST00000322507.13",
"protein_id": "ENSP00000325146.8",
"transcript_support_level": 1,
"aa_start": 989,
"aa_end": null,
"aa_length": 3063,
"cds_start": 2965,
"cds_end": null,
"cds_length": 9192,
"cdna_start": 3277,
"cdna_end": null,
"cdna_length": 11725,
"mane_select": "NM_004370.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.74-13043G>A",
"hgvs_p": null,
"transcript": "ENST00000345356.10",
"protein_id": "ENSP00000305147.9",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1899,
"cds_start": -4,
"cds_end": null,
"cds_length": 5700,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5886,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.2965G>A",
"hgvs_p": "p.Gly989Arg",
"transcript": "NM_001424113.1",
"protein_id": "NP_001411042.1",
"transcript_support_level": null,
"aa_start": 989,
"aa_end": null,
"aa_length": 3118,
"cds_start": 2965,
"cds_end": null,
"cds_length": 9357,
"cdna_start": 3277,
"cdna_end": null,
"cdna_length": 10533,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.2965G>A",
"hgvs_p": "p.Gly989Arg",
"transcript": "ENST00000483888.6",
"protein_id": "ENSP00000421216.1",
"transcript_support_level": 5,
"aa_start": 989,
"aa_end": null,
"aa_length": 3062,
"cds_start": 2965,
"cds_end": null,
"cds_length": 9189,
"cdna_start": 3046,
"cdna_end": null,
"cdna_length": 9637,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.2965G>A",
"hgvs_p": "p.Gly989Arg",
"transcript": "NM_001424114.1",
"protein_id": "NP_001411043.1",
"transcript_support_level": null,
"aa_start": 989,
"aa_end": null,
"aa_length": 3056,
"cds_start": 2965,
"cds_end": null,
"cds_length": 9171,
"cdna_start": 3277,
"cdna_end": null,
"cdna_length": 11704,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.2965G>A",
"hgvs_p": "p.Gly989Arg",
"transcript": "ENST00000416123.6",
"protein_id": "ENSP00000412864.2",
"transcript_support_level": 5,
"aa_start": 989,
"aa_end": null,
"aa_length": 2987,
"cds_start": 2965,
"cds_end": null,
"cds_length": 8964,
"cdna_start": 2965,
"cdna_end": null,
"cdna_length": 8964,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.2692G>A",
"hgvs_p": "p.Gly898Arg",
"transcript": "NM_001424115.1",
"protein_id": "NP_001411044.1",
"transcript_support_level": null,
"aa_start": 898,
"aa_end": null,
"aa_length": 2972,
"cds_start": 2692,
"cds_end": null,
"cds_length": 8919,
"cdna_start": 3004,
"cdna_end": null,
"cdna_length": 11452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.2965G>A",
"hgvs_p": "p.Gly989Arg",
"transcript": "XM_047418184.1",
"protein_id": "XP_047274140.1",
"transcript_support_level": null,
"aa_start": 989,
"aa_end": null,
"aa_length": 3118,
"cds_start": 2965,
"cds_end": null,
"cds_length": 9357,
"cdna_start": 3327,
"cdna_end": null,
"cdna_length": 10583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.2929G>A",
"hgvs_p": "p.Gly977Arg",
"transcript": "XM_017010252.3",
"protein_id": "XP_016865741.1",
"transcript_support_level": null,
"aa_start": 977,
"aa_end": null,
"aa_length": 3106,
"cds_start": 2929,
"cds_end": null,
"cds_length": 9321,
"cdna_start": 3524,
"cdna_end": null,
"cdna_length": 10780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.2692G>A",
"hgvs_p": "p.Gly898Arg",
"transcript": "XM_011535435.2",
"protein_id": "XP_011533737.1",
"transcript_support_level": null,
"aa_start": 898,
"aa_end": null,
"aa_length": 3027,
"cds_start": 2692,
"cds_end": null,
"cds_length": 9084,
"cdna_start": 3004,
"cdna_end": null,
"cdna_length": 10260,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.74-13043G>A",
"hgvs_p": null,
"transcript": "NM_001424116.1",
"protein_id": "NP_001411045.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1954,
"cds_start": -4,
"cds_end": null,
"cds_length": 5865,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7041,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.74-13043G>A",
"hgvs_p": null,
"transcript": "NM_080645.3",
"protein_id": "NP_542376.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1899,
"cds_start": -4,
"cds_end": null,
"cds_length": 5700,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8233,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.74-13043G>A",
"hgvs_p": null,
"transcript": "XM_047418186.1",
"protein_id": "XP_047274142.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1899,
"cds_start": -4,
"cds_end": null,
"cds_length": 5700,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8283,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"dbsnp": "rs139332405",
"frequency_reference_population": 0.0019031082,
"hom_count_reference_population": 2,
"allele_count_reference_population": 3071,
"gnomad_exomes_af": 0.00184203,
"gnomad_genomes_af": 0.00248939,
"gnomad_exomes_ac": 2692,
"gnomad_genomes_ac": 379,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.006268292665481567,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.593,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2956,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.04,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000322507.13",
"gene_symbol": "COL12A1",
"hgnc_id": 2188,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2965G>A",
"hgvs_p": "p.Gly989Arg"
}
],
"clinvar_disease": "Bethlem myopathy 2,COL12A1-related disorder,Ullrich congenital muscular dystrophy 2,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:1",
"phenotype_combined": "Bethlem myopathy 2;Ullrich congenital muscular dystrophy 2|not provided|COL12A1-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}