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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: 2-237372012-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=237372012&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 237372012,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000295550.9",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.4005C>T",
"hgvs_p": "p.Gly1335Gly",
"transcript": "NM_004369.4",
"protein_id": "NP_004360.2",
"transcript_support_level": null,
"aa_start": 1335,
"aa_end": null,
"aa_length": 3177,
"cds_start": 4005,
"cds_end": null,
"cds_length": 9534,
"cdna_start": 4247,
"cdna_end": null,
"cdna_length": 10532,
"mane_select": "ENST00000295550.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.4005C>T",
"hgvs_p": "p.Gly1335Gly",
"transcript": "ENST00000295550.9",
"protein_id": "ENSP00000295550.4",
"transcript_support_level": 1,
"aa_start": 1335,
"aa_end": null,
"aa_length": 3177,
"cds_start": 4005,
"cds_end": null,
"cds_length": 9534,
"cdna_start": 4247,
"cdna_end": null,
"cdna_length": 10532,
"mane_select": "NM_004369.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.2184C>T",
"hgvs_p": "p.Gly728Gly",
"transcript": "ENST00000472056.5",
"protein_id": "ENSP00000418285.1",
"transcript_support_level": 1,
"aa_start": 728,
"aa_end": null,
"aa_length": 2570,
"cds_start": 2184,
"cds_end": null,
"cds_length": 7713,
"cdna_start": 2410,
"cdna_end": null,
"cdna_length": 8628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.3387C>T",
"hgvs_p": "p.Gly1129Gly",
"transcript": "ENST00000392004.7",
"protein_id": "ENSP00000375861.3",
"transcript_support_level": 1,
"aa_start": 1129,
"aa_end": null,
"aa_length": 1237,
"cds_start": 3387,
"cds_end": null,
"cds_length": 3714,
"cdna_start": 3642,
"cdna_end": null,
"cdna_length": 4037,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.3387C>T",
"hgvs_p": "p.Gly1129Gly",
"transcript": "NM_057167.4",
"protein_id": "NP_476508.2",
"transcript_support_level": null,
"aa_start": 1129,
"aa_end": null,
"aa_length": 2971,
"cds_start": 3387,
"cds_end": null,
"cds_length": 8916,
"cdna_start": 3629,
"cdna_end": null,
"cdna_length": 9914,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.3387C>T",
"hgvs_p": "p.Gly1129Gly",
"transcript": "ENST00000353578.9",
"protein_id": "ENSP00000315873.4",
"transcript_support_level": 5,
"aa_start": 1129,
"aa_end": null,
"aa_length": 2971,
"cds_start": 3387,
"cds_end": null,
"cds_length": 8916,
"cdna_start": 3637,
"cdna_end": null,
"cdna_length": 9636,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.2184C>T",
"hgvs_p": "p.Gly728Gly",
"transcript": "NM_057166.5",
"protein_id": "NP_476507.3",
"transcript_support_level": null,
"aa_start": 728,
"aa_end": null,
"aa_length": 2570,
"cds_start": 2184,
"cds_end": null,
"cds_length": 7713,
"cdna_start": 2426,
"cdna_end": null,
"cdna_length": 8711,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.3387C>T",
"hgvs_p": "p.Gly1129Gly",
"transcript": "NM_057165.5",
"protein_id": "NP_476506.3",
"transcript_support_level": null,
"aa_start": 1129,
"aa_end": null,
"aa_length": 1237,
"cds_start": 3387,
"cds_end": null,
"cds_length": 3714,
"cdna_start": 3629,
"cdna_end": null,
"cdna_length": 4024,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.2784C>T",
"hgvs_p": "p.Gly928Gly",
"transcript": "NM_057164.5",
"protein_id": "NP_476505.3",
"transcript_support_level": null,
"aa_start": 928,
"aa_end": null,
"aa_length": 1036,
"cds_start": 2784,
"cds_end": null,
"cds_length": 3111,
"cdna_start": 3026,
"cdna_end": null,
"cdna_length": 3421,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.2784C>T",
"hgvs_p": "p.Gly928Gly",
"transcript": "ENST00000392003.6",
"protein_id": "ENSP00000375860.2",
"transcript_support_level": 2,
"aa_start": 928,
"aa_end": null,
"aa_length": 1036,
"cds_start": 2784,
"cds_end": null,
"cds_length": 3111,
"cdna_start": 3069,
"cdna_end": null,
"cdna_length": 3464,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.-166C>T",
"hgvs_p": null,
"transcript": "ENST00000684597.1",
"protein_id": "ENSP00000508021.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 136,
"cds_start": -4,
"cds_end": null,
"cds_length": 413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 414,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"dbsnp": "rs34503558",
"frequency_reference_population": 0.0018338802,
"hom_count_reference_population": 57,
"allele_count_reference_population": 2960,
"gnomad_exomes_af": 0.00104737,
"gnomad_genomes_af": 0.00938267,
"gnomad_exomes_ac": 1531,
"gnomad_genomes_ac": 1429,
"gnomad_exomes_homalt": 25,
"gnomad_genomes_homalt": 32,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7699999809265137,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.77,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -5.493,
"phylop100way_prediction": "Benign",
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000295550.9",
"gene_symbol": "COL6A3",
"hgnc_id": 2213,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "c.4005C>T",
"hgvs_p": "p.Gly1335Gly"
}
],
"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:2 B:3",
"phenotype_combined": "not specified|Bethlem myopathy 1A|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}