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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: 2-237344571-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=237344571&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 237344571,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_004369.4",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.7447A>G",
"hgvs_p": "p.Lys2483Glu",
"transcript": "NM_004369.4",
"protein_id": "NP_004360.2",
"transcript_support_level": null,
"aa_start": 2483,
"aa_end": null,
"aa_length": 3177,
"cds_start": 7447,
"cds_end": null,
"cds_length": 9534,
"cdna_start": 7689,
"cdna_end": null,
"cdna_length": 10532,
"mane_select": "ENST00000295550.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004369.4"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.7447A>G",
"hgvs_p": "p.Lys2483Glu",
"transcript": "ENST00000295550.9",
"protein_id": "ENSP00000295550.4",
"transcript_support_level": 1,
"aa_start": 2483,
"aa_end": null,
"aa_length": 3177,
"cds_start": 7447,
"cds_end": null,
"cds_length": 9534,
"cdna_start": 7689,
"cdna_end": null,
"cdna_length": 10532,
"mane_select": "NM_004369.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000295550.9"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.5626A>G",
"hgvs_p": "p.Lys1876Glu",
"transcript": "ENST00000472056.5",
"protein_id": "ENSP00000418285.1",
"transcript_support_level": 1,
"aa_start": 1876,
"aa_end": null,
"aa_length": 2570,
"cds_start": 5626,
"cds_end": null,
"cds_length": 7713,
"cdna_start": 5852,
"cdna_end": null,
"cdna_length": 8628,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000472056.5"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.6829A>G",
"hgvs_p": "p.Lys2277Glu",
"transcript": "NM_057167.4",
"protein_id": "NP_476508.2",
"transcript_support_level": null,
"aa_start": 2277,
"aa_end": null,
"aa_length": 2971,
"cds_start": 6829,
"cds_end": null,
"cds_length": 8916,
"cdna_start": 7071,
"cdna_end": null,
"cdna_length": 9914,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_057167.4"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.6829A>G",
"hgvs_p": "p.Lys2277Glu",
"transcript": "ENST00000353578.9",
"protein_id": "ENSP00000315873.4",
"transcript_support_level": 5,
"aa_start": 2277,
"aa_end": null,
"aa_length": 2971,
"cds_start": 6829,
"cds_end": null,
"cds_length": 8916,
"cdna_start": 7079,
"cdna_end": null,
"cdna_length": 9636,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000353578.9"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.5626A>G",
"hgvs_p": "p.Lys1876Glu",
"transcript": "NM_057166.5",
"protein_id": "NP_476507.3",
"transcript_support_level": null,
"aa_start": 1876,
"aa_end": null,
"aa_length": 2570,
"cds_start": 5626,
"cds_end": null,
"cds_length": 7713,
"cdna_start": 5868,
"cdna_end": null,
"cdna_length": 8711,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_057166.5"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.5623A>G",
"hgvs_p": "p.Lys1875Glu",
"transcript": "ENST00000952249.1",
"protein_id": "ENSP00000622308.1",
"transcript_support_level": null,
"aa_start": 1875,
"aa_end": null,
"aa_length": 2569,
"cds_start": 5623,
"cds_end": null,
"cds_length": 7710,
"cdna_start": 6106,
"cdna_end": null,
"cdna_length": 8948,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952249.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.5197A>G",
"hgvs_p": "p.Lys1733Glu",
"transcript": "ENST00000952251.1",
"protein_id": "ENSP00000622310.1",
"transcript_support_level": null,
"aa_start": 1733,
"aa_end": null,
"aa_length": 2427,
"cds_start": 5197,
"cds_end": null,
"cds_length": 7284,
"cdna_start": 5446,
"cdna_end": null,
"cdna_length": 8290,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952251.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.5041A>G",
"hgvs_p": "p.Lys1681Glu",
"transcript": "ENST00000952252.1",
"protein_id": "ENSP00000622311.1",
"transcript_support_level": null,
"aa_start": 1681,
"aa_end": null,
"aa_length": 2375,
"cds_start": 5041,
"cds_end": null,
"cds_length": 7128,
"cdna_start": 5290,
"cdna_end": null,
"cdna_length": 8133,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952252.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.91A>G",
"hgvs_p": "p.Lys31Glu",
"transcript": "ENST00000347401.8",
"protein_id": "ENSP00000315609.5",
"transcript_support_level": 5,
"aa_start": 31,
"aa_end": null,
"aa_length": 637,
"cds_start": 91,
"cds_end": null,
"cds_length": 1914,
"cdna_start": 92,
"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": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.2465-18847A>G",
"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": [
"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.92-18847A>G",
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "n.1701A>G",
"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"
}
],
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"dbsnp": "rs139260335",
"frequency_reference_population": 0.0007174321,
"hom_count_reference_population": 1,
"allele_count_reference_population": 1158,
"gnomad_exomes_af": 0.000736717,
"gnomad_genomes_af": 0.000532201,
"gnomad_exomes_ac": 1077,
"gnomad_genomes_ac": 81,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4271813631057739,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.827,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5501,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.93,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PP5_Very_Strong,BS1_Supporting",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 1,
"pathogenic_score": 8,
"criteria": [
"PP5_Very_Strong",
"BS1_Supporting"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_004369.4",
"gene_symbol": "COL6A3",
"hgnc_id": 2213,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,SD",
"hgvs_c": "c.7447A>G",
"hgvs_p": "p.Lys2483Glu"
}
],
"clinvar_disease": "Bethlem myopathy 1A,Bethlem myopathy 1C,COL6A3-related disorder,Dystonia 27,Ullrich congenital muscular dystrophy 1A,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4 LP:10 US:2",
"phenotype_combined": "not provided|Bethlem myopathy 1A|COL6A3-related disorder|Bethlem myopathy 1C|Ullrich congenital muscular dystrophy 1A|Dystonia 27",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}