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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: 2-237360131-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=237360131&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "COL6A3",
"hgnc_id": 2213,
"hgvs_c": "c.6239G>T",
"hgvs_p": "p.Gly2080Val",
"inheritance_mode": "AR,AD,SD",
"pathogenic_score": 10,
"score": 10,
"transcript": "NM_004369.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Strong",
"acmg_score": 10,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.9907,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.57,
"chr": "2",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Bethlem myopathy 1A",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9938234686851501,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 3177,
"aa_ref": "G",
"aa_start": 2080,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10532,
"cdna_start": 6481,
"cds_end": null,
"cds_length": 9534,
"cds_start": 6239,
"consequences": [
"missense_variant"
],
"exon_count": 44,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_004369.4",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.6239G>T",
"hgvs_p": "p.Gly2080Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000295550.9",
"protein_coding": true,
"protein_id": "NP_004360.2",
"strand": false,
"transcript": "NM_004369.4",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 3177,
"aa_ref": "G",
"aa_start": 2080,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 10532,
"cdna_start": 6481,
"cds_end": null,
"cds_length": 9534,
"cds_start": 6239,
"consequences": [
"missense_variant"
],
"exon_count": 44,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000295550.9",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.6239G>T",
"hgvs_p": "p.Gly2080Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004369.4",
"protein_coding": true,
"protein_id": "ENSP00000295550.4",
"strand": false,
"transcript": "ENST00000295550.9",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 2570,
"aa_ref": "G",
"aa_start": 1473,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8628,
"cdna_start": 4644,
"cds_end": null,
"cds_length": 7713,
"cds_start": 4418,
"consequences": [
"missense_variant"
],
"exon_count": 41,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000472056.5",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.4418G>T",
"hgvs_p": "p.Gly1473Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000418285.1",
"strand": false,
"transcript": "ENST00000472056.5",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 2971,
"aa_ref": "G",
"aa_start": 1874,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9914,
"cdna_start": 5863,
"cds_end": null,
"cds_length": 8916,
"cds_start": 5621,
"consequences": [
"missense_variant"
],
"exon_count": 43,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "NM_057167.4",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.5621G>T",
"hgvs_p": "p.Gly1874Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_476508.2",
"strand": false,
"transcript": "NM_057167.4",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 2971,
"aa_ref": "G",
"aa_start": 1874,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9636,
"cdna_start": 5871,
"cds_end": null,
"cds_length": 8916,
"cds_start": 5621,
"consequences": [
"missense_variant"
],
"exon_count": 43,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000353578.9",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.5621G>T",
"hgvs_p": "p.Gly1874Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000315873.4",
"strand": false,
"transcript": "ENST00000353578.9",
"transcript_support_level": 5
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 2570,
"aa_ref": "G",
"aa_start": 1473,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8711,
"cdna_start": 4660,
"cds_end": null,
"cds_length": 7713,
"cds_start": 4418,
"consequences": [
"missense_variant"
],
"exon_count": 41,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "NM_057166.5",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.4418G>T",
"hgvs_p": "p.Gly1473Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_476507.3",
"strand": false,
"transcript": "NM_057166.5",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 2569,
"aa_ref": "G",
"aa_start": 1472,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8948,
"cdna_start": 4898,
"cds_end": null,
"cds_length": 7710,
"cds_start": 4415,
"consequences": [
"missense_variant"
],
"exon_count": 41,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000952249.1",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.4415G>T",
"hgvs_p": "p.Gly1472Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622308.1",
"strand": false,
"transcript": "ENST00000952249.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 2427,
"aa_ref": "G",
"aa_start": 1330,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8290,
"cdna_start": 4238,
"cds_end": null,
"cds_length": 7284,
"cds_start": 3989,
"consequences": [
"missense_variant"
],
"exon_count": 41,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000952251.1",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.3989G>T",
"hgvs_p": "p.Gly1330Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622310.1",
"strand": false,
"transcript": "ENST00000952251.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 2375,
"aa_ref": "G",
"aa_start": 1278,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8133,
"cdna_start": 4082,
"cds_end": null,
"cds_length": 7128,
"cds_start": 3833,
"consequences": [
"missense_variant"
],
"exon_count": 40,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000952252.1",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.3833G>T",
"hgvs_p": "p.Gly1278Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622311.1",
"strand": false,
"transcript": "ENST00000952252.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 889,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3776,
"cdna_start": null,
"cds_end": null,
"cds_length": 2670,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000952250.1",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.2464+11601G>T",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622309.1",
"strand": false,
"transcript": "ENST00000952250.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 98,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1140,
"cdna_start": null,
"cds_end": null,
"cds_length": 297,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000888366.1",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.92-34407G>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000558425.1",
"strand": false,
"transcript": "ENST00000888366.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs794727188",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Bethlem myopathy 1A",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.199,
"pos": 237360131,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.995,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_004369.4"
}
]
}