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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: 6-75123360-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=75123360&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 75123360,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000322507.13",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.6916C>T",
"hgvs_p": "p.Pro2306Ser",
"transcript": "NM_004370.6",
"protein_id": "NP_004361.3",
"transcript_support_level": null,
"aa_start": 2306,
"aa_end": null,
"aa_length": 3063,
"cds_start": 6916,
"cds_end": null,
"cds_length": 9192,
"cdna_start": 7228,
"cdna_end": null,
"cdna_length": 11725,
"mane_select": "ENST00000322507.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.6916C>T",
"hgvs_p": "p.Pro2306Ser",
"transcript": "ENST00000322507.13",
"protein_id": "ENSP00000325146.8",
"transcript_support_level": 1,
"aa_start": 2306,
"aa_end": null,
"aa_length": 3063,
"cds_start": 6916,
"cds_end": null,
"cds_length": 9192,
"cdna_start": 7228,
"cdna_end": null,
"cdna_length": 11725,
"mane_select": "NM_004370.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.3424C>T",
"hgvs_p": "p.Pro1142Ser",
"transcript": "ENST00000345356.10",
"protein_id": "ENSP00000305147.9",
"transcript_support_level": 1,
"aa_start": 1142,
"aa_end": null,
"aa_length": 1899,
"cds_start": 3424,
"cds_end": null,
"cds_length": 5700,
"cdna_start": 3534,
"cdna_end": null,
"cdna_length": 5886,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.6916C>T",
"hgvs_p": "p.Pro2306Ser",
"transcript": "NM_001424113.1",
"protein_id": "NP_001411042.1",
"transcript_support_level": null,
"aa_start": 2306,
"aa_end": null,
"aa_length": 3118,
"cds_start": 6916,
"cds_end": null,
"cds_length": 9357,
"cdna_start": 7228,
"cdna_end": null,
"cdna_length": 10533,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.6916C>T",
"hgvs_p": "p.Pro2306Ser",
"transcript": "ENST00000483888.6",
"protein_id": "ENSP00000421216.1",
"transcript_support_level": 5,
"aa_start": 2306,
"aa_end": null,
"aa_length": 3062,
"cds_start": 6916,
"cds_end": null,
"cds_length": 9189,
"cdna_start": 6997,
"cdna_end": null,
"cdna_length": 9637,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.6895C>T",
"hgvs_p": "p.Pro2299Ser",
"transcript": "NM_001424114.1",
"protein_id": "NP_001411043.1",
"transcript_support_level": null,
"aa_start": 2299,
"aa_end": null,
"aa_length": 3056,
"cds_start": 6895,
"cds_end": null,
"cds_length": 9171,
"cdna_start": 7207,
"cdna_end": null,
"cdna_length": 11704,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.6916C>T",
"hgvs_p": "p.Pro2306Ser",
"transcript": "ENST00000416123.6",
"protein_id": "ENSP00000412864.2",
"transcript_support_level": 5,
"aa_start": 2306,
"aa_end": null,
"aa_length": 2987,
"cds_start": 6916,
"cds_end": null,
"cds_length": 8964,
"cdna_start": 6916,
"cdna_end": null,
"cdna_length": 8964,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.6643C>T",
"hgvs_p": "p.Pro2215Ser",
"transcript": "NM_001424115.1",
"protein_id": "NP_001411044.1",
"transcript_support_level": null,
"aa_start": 2215,
"aa_end": null,
"aa_length": 2972,
"cds_start": 6643,
"cds_end": null,
"cds_length": 8919,
"cdna_start": 6955,
"cdna_end": null,
"cdna_length": 11452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.3424C>T",
"hgvs_p": "p.Pro1142Ser",
"transcript": "NM_001424116.1",
"protein_id": "NP_001411045.1",
"transcript_support_level": null,
"aa_start": 1142,
"aa_end": null,
"aa_length": 1954,
"cds_start": 3424,
"cds_end": null,
"cds_length": 5865,
"cdna_start": 3736,
"cdna_end": null,
"cdna_length": 7041,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.3424C>T",
"hgvs_p": "p.Pro1142Ser",
"transcript": "NM_080645.3",
"protein_id": "NP_542376.2",
"transcript_support_level": null,
"aa_start": 1142,
"aa_end": null,
"aa_length": 1899,
"cds_start": 3424,
"cds_end": null,
"cds_length": 5700,
"cdna_start": 3736,
"cdna_end": null,
"cdna_length": 8233,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.6916C>T",
"hgvs_p": "p.Pro2306Ser",
"transcript": "XM_047418184.1",
"protein_id": "XP_047274140.1",
"transcript_support_level": null,
"aa_start": 2306,
"aa_end": null,
"aa_length": 3118,
"cds_start": 6916,
"cds_end": null,
"cds_length": 9357,
"cdna_start": 7278,
"cdna_end": null,
"cdna_length": 10583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.6880C>T",
"hgvs_p": "p.Pro2294Ser",
"transcript": "XM_017010252.3",
"protein_id": "XP_016865741.1",
"transcript_support_level": null,
"aa_start": 2294,
"aa_end": null,
"aa_length": 3106,
"cds_start": 6880,
"cds_end": null,
"cds_length": 9321,
"cdna_start": 7475,
"cdna_end": null,
"cdna_length": 10780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.6643C>T",
"hgvs_p": "p.Pro2215Ser",
"transcript": "XM_011535435.2",
"protein_id": "XP_011533737.1",
"transcript_support_level": null,
"aa_start": 2215,
"aa_end": null,
"aa_length": 3027,
"cds_start": 6643,
"cds_end": null,
"cds_length": 9084,
"cdna_start": 6955,
"cdna_end": null,
"cdna_length": 10260,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"hgvs_c": "c.3424C>T",
"hgvs_p": "p.Pro1142Ser",
"transcript": "XM_047418186.1",
"protein_id": "XP_047274142.1",
"transcript_support_level": null,
"aa_start": 1142,
"aa_end": null,
"aa_length": 1899,
"cds_start": 3424,
"cds_end": null,
"cds_length": 5700,
"cdna_start": 3786,
"cdna_end": null,
"cdna_length": 8283,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL12A1",
"gene_hgnc_id": 2188,
"dbsnp": "rs1554171436",
"frequency_reference_population": 0.0000013744703,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000137447,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3102739453315735,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.192,
"revel_prediction": "Benign",
"alphamissense_score": 0.1831,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.011,
"phylop100way_prediction": "Uncertain_significance",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000322507.13",
"gene_symbol": "COL12A1",
"hgnc_id": 2188,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.6916C>T",
"hgvs_p": "p.Pro2306Ser"
}
],
"clinvar_disease": "Bethlem myopathy 2,Ullrich congenital muscular dystrophy 2",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Ullrich congenital muscular dystrophy 2;Bethlem myopathy 2",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}