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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: 2-237339123-G-GA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=237339123&ref=G&alt=GA&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 237339123,
"ref": "G",
"alt": "GA",
"effect": "splice_region_variant,intron_variant",
"transcript": "NM_004369.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": 38,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.8465-7dupT",
"hgvs_p": null,
"transcript": "NM_004369.4",
"protein_id": "NP_004360.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3177,
"cds_start": null,
"cds_end": null,
"cds_length": 9534,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10532,
"mane_select": "ENST00000295550.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004369.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": 38,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.8465-7_8465-6insT",
"hgvs_p": null,
"transcript": "ENST00000295550.9",
"protein_id": "ENSP00000295550.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 3177,
"cds_start": null,
"cds_end": null,
"cds_length": 9534,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10532,
"mane_select": "NM_004369.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000295550.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": 35,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.6644-7_6644-6insT",
"hgvs_p": null,
"transcript": "ENST00000472056.5",
"protein_id": "ENSP00000418285.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 2570,
"cds_start": null,
"cds_end": null,
"cds_length": 7713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8628,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000472056.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.7847-7dupT",
"hgvs_p": null,
"transcript": "NM_057167.4",
"protein_id": "NP_476508.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2971,
"cds_start": null,
"cds_end": null,
"cds_length": 8916,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9914,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_057167.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": 37,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.7847-7_7847-6insT",
"hgvs_p": null,
"transcript": "ENST00000353578.9",
"protein_id": "ENSP00000315873.4",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 2971,
"cds_start": null,
"cds_end": null,
"cds_length": 8916,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9636,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000353578.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": 35,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.6644-7dupT",
"hgvs_p": null,
"transcript": "NM_057166.5",
"protein_id": "NP_476507.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2570,
"cds_start": null,
"cds_end": null,
"cds_length": 7713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8711,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_057166.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": 35,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.6641-7_6641-6insT",
"hgvs_p": null,
"transcript": "ENST00000952249.1",
"protein_id": "ENSP00000622308.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2569,
"cds_start": null,
"cds_end": null,
"cds_length": 7710,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8948,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952249.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": 35,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.6215-7_6215-6insT",
"hgvs_p": null,
"transcript": "ENST00000952251.1",
"protein_id": "ENSP00000622310.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2427,
"cds_start": null,
"cds_end": null,
"cds_length": 7284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8290,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952251.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": 34,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.6059-7_6059-6insT",
"hgvs_p": null,
"transcript": "ENST00000952252.1",
"protein_id": "ENSP00000622311.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2375,
"cds_start": null,
"cds_end": null,
"cds_length": 7128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8133,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952252.1"
},
{
"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": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.2465-13400_2465-13399insT",
"hgvs_p": null,
"transcript": "ENST00000952250.1",
"protein_id": "ENSP00000622309.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 889,
"cds_start": null,
"cds_end": null,
"cds_length": 2670,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3776,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952250.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.1109-7_1109-6insT",
"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": null,
"cds_end": null,
"cds_length": 1914,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2670,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000347401.8"
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.92-13400_92-13399insT",
"hgvs_p": null,
"transcript": "ENST00000888366.1",
"protein_id": "ENSP00000558425.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 98,
"cds_start": null,
"cds_end": null,
"cds_length": 297,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1140,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000888366.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "n.152-7_152-6insT",
"hgvs_p": null,
"transcript": "ENST00000468792.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 329,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000468792.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "n.4907-7_4907-6insT",
"hgvs_p": null,
"transcript": "ENST00000491769.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6731,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000491769.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "n.467-7_467-6insT",
"hgvs_p": null,
"transcript": "ENST00000682957.1",
"protein_id": "ENSP00000507870.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2416,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000682957.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "n.732-7_732-6insT",
"hgvs_p": null,
"transcript": "ENST00000684508.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1341,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000684508.1"
}
],
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"dbsnp": "rs111494366",
"frequency_reference_population": 0.00017034751,
"hom_count_reference_population": 1,
"allele_count_reference_population": 272,
"gnomad_exomes_af": 0.00017645,
"gnomad_genomes_af": 0.000112161,
"gnomad_exomes_ac": 255,
"gnomad_genomes_ac": 17,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 1.509,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.06,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP6_Very_Strong,BS1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP6_Very_Strong",
"BS1"
],
"verdict": "Benign",
"transcript": "NM_004369.4",
"gene_symbol": "COL6A3",
"hgnc_id": 2213,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR,AD,SD",
"hgvs_c": "c.8465-7dupT",
"hgvs_p": null
}
],
"clinvar_disease": "Bethlem myopathy 1A,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:1",
"phenotype_combined": "not specified|Bethlem myopathy 1A|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}