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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: 2-237344505-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=237344505&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BS1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "COL6A3",
"hgnc_id": 2213,
"hgvs_c": "c.7513G>A",
"hgvs_p": "p.Gly2505Arg",
"inheritance_mode": "AR,AD,SD",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_004369.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS1",
"acmg_score": -4,
"allele_count_reference_population": 88,
"alphamissense_prediction": null,
"alphamissense_score": 0.9428,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.39,
"chr": "2",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Bethlem myopathy 1A,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 LB:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5504268407821655,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 3177,
"aa_ref": "G",
"aa_start": 2505,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10532,
"cdna_start": 7755,
"cds_end": null,
"cds_length": 9534,
"cds_start": 7513,
"consequences": [
"missense_variant"
],
"exon_count": 44,
"exon_rank": 36,
"exon_rank_end": null,
"feature": "NM_004369.4",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.7513G>A",
"hgvs_p": "p.Gly2505Arg",
"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": "R",
"aa_end": null,
"aa_length": 3177,
"aa_ref": "G",
"aa_start": 2505,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 10532,
"cdna_start": 7755,
"cds_end": null,
"cds_length": 9534,
"cds_start": 7513,
"consequences": [
"missense_variant"
],
"exon_count": 44,
"exon_rank": 36,
"exon_rank_end": null,
"feature": "ENST00000295550.9",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.7513G>A",
"hgvs_p": "p.Gly2505Arg",
"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": "R",
"aa_end": null,
"aa_length": 2570,
"aa_ref": "G",
"aa_start": 1898,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8628,
"cdna_start": 5918,
"cds_end": null,
"cds_length": 7713,
"cds_start": 5692,
"consequences": [
"missense_variant"
],
"exon_count": 41,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "ENST00000472056.5",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.5692G>A",
"hgvs_p": "p.Gly1898Arg",
"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": "R",
"aa_end": null,
"aa_length": 2971,
"aa_ref": "G",
"aa_start": 2299,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9914,
"cdna_start": 7137,
"cds_end": null,
"cds_length": 8916,
"cds_start": 6895,
"consequences": [
"missense_variant"
],
"exon_count": 43,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "NM_057167.4",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.6895G>A",
"hgvs_p": "p.Gly2299Arg",
"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": "R",
"aa_end": null,
"aa_length": 2971,
"aa_ref": "G",
"aa_start": 2299,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9636,
"cdna_start": 7145,
"cds_end": null,
"cds_length": 8916,
"cds_start": 6895,
"consequences": [
"missense_variant"
],
"exon_count": 43,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "ENST00000353578.9",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.6895G>A",
"hgvs_p": "p.Gly2299Arg",
"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": "R",
"aa_end": null,
"aa_length": 2570,
"aa_ref": "G",
"aa_start": 1898,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8711,
"cdna_start": 5934,
"cds_end": null,
"cds_length": 7713,
"cds_start": 5692,
"consequences": [
"missense_variant"
],
"exon_count": 41,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "NM_057166.5",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.5692G>A",
"hgvs_p": "p.Gly1898Arg",
"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": "R",
"aa_end": null,
"aa_length": 2569,
"aa_ref": "G",
"aa_start": 1897,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8948,
"cdna_start": 6172,
"cds_end": null,
"cds_length": 7710,
"cds_start": 5689,
"consequences": [
"missense_variant"
],
"exon_count": 41,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "ENST00000952249.1",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.5689G>A",
"hgvs_p": "p.Gly1897Arg",
"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": "R",
"aa_end": null,
"aa_length": 2427,
"aa_ref": "G",
"aa_start": 1755,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8290,
"cdna_start": 5512,
"cds_end": null,
"cds_length": 7284,
"cds_start": 5263,
"consequences": [
"missense_variant"
],
"exon_count": 41,
"exon_rank": 33,
"exon_rank_end": null,
"feature": "ENST00000952251.1",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.5263G>A",
"hgvs_p": "p.Gly1755Arg",
"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": "R",
"aa_end": null,
"aa_length": 2375,
"aa_ref": "G",
"aa_start": 1703,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8133,
"cdna_start": 5356,
"cds_end": null,
"cds_length": 7128,
"cds_start": 5107,
"consequences": [
"missense_variant"
],
"exon_count": 40,
"exon_rank": 32,
"exon_rank_end": null,
"feature": "ENST00000952252.1",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.5107G>A",
"hgvs_p": "p.Gly1703Arg",
"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": "R",
"aa_end": null,
"aa_length": 637,
"aa_ref": "G",
"aa_start": 53,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2670,
"cdna_start": 158,
"cds_end": null,
"cds_length": 1914,
"cds_start": 157,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000347401.8",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.157G>A",
"hgvs_p": "p.Gly53Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000315609.5",
"strand": false,
"transcript": "ENST00000347401.8",
"transcript_support_level": 5
},
{
"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.2465-18781G>A",
"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.92-18781G>A",
"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
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 6731,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 20,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000491769.1",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "n.1767G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000491769.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs545819982",
"effect": "missense_variant",
"frequency_reference_population": 0.00005451644,
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"gnomad_exomes_ac": 53,
"gnomad_exomes_af": 0.0000362545,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 35,
"gnomad_genomes_af": 0.000229801,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not provided|Bethlem myopathy 1A",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.696,
"pos": 237344505,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.405,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_004369.4"
}
]
}