← Back to variant description
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: 2-237376978-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=237376978&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "COL6A3",
"hgnc_id": 2213,
"hgvs_c": "c.2864G>A",
"hgvs_p": "p.Arg955His",
"inheritance_mode": "AR,AD,SD",
"pathogenic_score": 0,
"score": -1,
"transcript": "NM_004369.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4",
"acmg_score": -1,
"allele_count_reference_population": 118,
"alphamissense_prediction": null,
"alphamissense_score": 0.0788,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.38,
"chr": "2",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Bethlem myopathy 1A,Collagen 6-related myopathy,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:5 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.34483832120895386,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 3177,
"aa_ref": "R",
"aa_start": 955,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10532,
"cdna_start": 3106,
"cds_end": null,
"cds_length": 9534,
"cds_start": 2864,
"consequences": [
"missense_variant"
],
"exon_count": 44,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_004369.4",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.2864G>A",
"hgvs_p": "p.Arg955His",
"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": "H",
"aa_end": null,
"aa_length": 3177,
"aa_ref": "R",
"aa_start": 955,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 10532,
"cdna_start": 3106,
"cds_end": null,
"cds_length": 9534,
"cds_start": 2864,
"consequences": [
"missense_variant"
],
"exon_count": 44,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000295550.9",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.2864G>A",
"hgvs_p": "p.Arg955His",
"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": "H",
"aa_end": null,
"aa_length": 2570,
"aa_ref": "R",
"aa_start": 348,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8628,
"cdna_start": 1269,
"cds_end": null,
"cds_length": 7713,
"cds_start": 1043,
"consequences": [
"missense_variant"
],
"exon_count": 41,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000472056.5",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.1043G>A",
"hgvs_p": "p.Arg348His",
"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": "H",
"aa_end": null,
"aa_length": 1237,
"aa_ref": "R",
"aa_start": 749,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4037,
"cdna_start": 2501,
"cds_end": null,
"cds_length": 3714,
"cds_start": 2246,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000392004.7",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.2246G>A",
"hgvs_p": "p.Arg749His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000375861.3",
"strand": false,
"transcript": "ENST00000392004.7",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 2971,
"aa_ref": "R",
"aa_start": 749,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9914,
"cdna_start": 2488,
"cds_end": null,
"cds_length": 8916,
"cds_start": 2246,
"consequences": [
"missense_variant"
],
"exon_count": 43,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_057167.4",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.2246G>A",
"hgvs_p": "p.Arg749His",
"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": "H",
"aa_end": null,
"aa_length": 2971,
"aa_ref": "R",
"aa_start": 749,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9636,
"cdna_start": 2496,
"cds_end": null,
"cds_length": 8916,
"cds_start": 2246,
"consequences": [
"missense_variant"
],
"exon_count": 43,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000353578.9",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.2246G>A",
"hgvs_p": "p.Arg749His",
"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": "H",
"aa_end": null,
"aa_length": 2570,
"aa_ref": "R",
"aa_start": 348,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8711,
"cdna_start": 1285,
"cds_end": null,
"cds_length": 7713,
"cds_start": 1043,
"consequences": [
"missense_variant"
],
"exon_count": 41,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_057166.5",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.1043G>A",
"hgvs_p": "p.Arg348His",
"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": "H",
"aa_end": null,
"aa_length": 2569,
"aa_ref": "R",
"aa_start": 348,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8948,
"cdna_start": 1526,
"cds_end": null,
"cds_length": 7710,
"cds_start": 1043,
"consequences": [
"missense_variant"
],
"exon_count": 41,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000952249.1",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.1043G>A",
"hgvs_p": "p.Arg348His",
"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": "H",
"aa_end": null,
"aa_length": 2427,
"aa_ref": "R",
"aa_start": 348,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8290,
"cdna_start": 1292,
"cds_end": null,
"cds_length": 7284,
"cds_start": 1043,
"consequences": [
"missense_variant"
],
"exon_count": 41,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000952251.1",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.1043G>A",
"hgvs_p": "p.Arg348His",
"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": "H",
"aa_end": null,
"aa_length": 2375,
"aa_ref": "R",
"aa_start": 153,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8133,
"cdna_start": 707,
"cds_end": null,
"cds_length": 7128,
"cds_start": 458,
"consequences": [
"missense_variant"
],
"exon_count": 40,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000952252.1",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.458G>A",
"hgvs_p": "p.Arg153His",
"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": "H",
"aa_end": null,
"aa_length": 1237,
"aa_ref": "R",
"aa_start": 749,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4024,
"cdna_start": 2488,
"cds_end": null,
"cds_length": 3714,
"cds_start": 2246,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_057165.5",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.2246G>A",
"hgvs_p": "p.Arg749His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_476506.3",
"strand": false,
"transcript": "NM_057165.5",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1036,
"aa_ref": "R",
"aa_start": 548,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3421,
"cdna_start": 1885,
"cds_end": null,
"cds_length": 3111,
"cds_start": 1643,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_057164.5",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.1643G>A",
"hgvs_p": "p.Arg548His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_476505.3",
"strand": false,
"transcript": "NM_057164.5",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1036,
"aa_ref": "R",
"aa_start": 548,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3464,
"cdna_start": 1928,
"cds_end": null,
"cds_length": 3111,
"cds_start": 1643,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000392003.6",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.1643G>A",
"hgvs_p": "p.Arg548His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000375860.2",
"strand": false,
"transcript": "ENST00000392003.6",
"transcript_support_level": 2
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 889,
"aa_ref": "R",
"aa_start": 348,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3776,
"cdna_start": 1396,
"cds_end": null,
"cds_length": 2670,
"cds_start": 1043,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000952250.1",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.1043G>A",
"hgvs_p": "p.Arg348His",
"intron_rank": null,
"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.91+19749G>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": 707,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2379,
"cdna_start": null,
"cds_end": null,
"cds_length": 2124,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000433762.1",
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"hgvs_c": "c.*140G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000389539.1",
"strand": true,
"transcript": "ENST00000433762.1",
"transcript_support_level": 1
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs112172548",
"effect": "missense_variant",
"frequency_reference_population": 0.00007310476,
"gene_hgnc_id": 2213,
"gene_symbol": "COL6A3",
"gnomad_exomes_ac": 107,
"gnomad_exomes_af": 0.0000731927,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 11,
"gnomad_genomes_af": 0.00007226,
"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|not specified|Collagen 6-related myopathy",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.158,
"pos": 237376978,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.722,
"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"
}
]
}