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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: 2-237366926-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=237366926&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 237366926,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_004369.4",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.5261A>T",
"hgvs_p": "p.Lys1754Met",
"transcript": "NM_004369.4",
"protein_id": "NP_004360.2",
"transcript_support_level": null,
"aa_start": 1754,
"aa_end": null,
"aa_length": 3177,
"cds_start": 5261,
"cds_end": null,
"cds_length": 9534,
"cdna_start": 5503,
"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": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.5261A>T",
"hgvs_p": "p.Lys1754Met",
"transcript": "ENST00000295550.9",
"protein_id": "ENSP00000295550.4",
"transcript_support_level": 1,
"aa_start": 1754,
"aa_end": null,
"aa_length": 3177,
"cds_start": 5261,
"cds_end": null,
"cds_length": 9534,
"cdna_start": 5503,
"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": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.3440A>T",
"hgvs_p": "p.Lys1147Met",
"transcript": "ENST00000472056.5",
"protein_id": "ENSP00000418285.1",
"transcript_support_level": 1,
"aa_start": 1147,
"aa_end": null,
"aa_length": 2570,
"cds_start": 3440,
"cds_end": null,
"cds_length": 7713,
"cdna_start": 3666,
"cdna_end": null,
"cdna_length": 8628,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000472056.5"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.4643A>T",
"hgvs_p": "p.Lys1548Met",
"transcript": "NM_057167.4",
"protein_id": "NP_476508.2",
"transcript_support_level": null,
"aa_start": 1548,
"aa_end": null,
"aa_length": 2971,
"cds_start": 4643,
"cds_end": null,
"cds_length": 8916,
"cdna_start": 4885,
"cdna_end": null,
"cdna_length": 9914,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_057167.4"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.4643A>T",
"hgvs_p": "p.Lys1548Met",
"transcript": "ENST00000353578.9",
"protein_id": "ENSP00000315873.4",
"transcript_support_level": 5,
"aa_start": 1548,
"aa_end": null,
"aa_length": 2971,
"cds_start": 4643,
"cds_end": null,
"cds_length": 8916,
"cdna_start": 4893,
"cdna_end": null,
"cdna_length": 9636,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000353578.9"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.3440A>T",
"hgvs_p": "p.Lys1147Met",
"transcript": "NM_057166.5",
"protein_id": "NP_476507.3",
"transcript_support_level": null,
"aa_start": 1147,
"aa_end": null,
"aa_length": 2570,
"cds_start": 3440,
"cds_end": null,
"cds_length": 7713,
"cdna_start": 3682,
"cdna_end": null,
"cdna_length": 8711,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_057166.5"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.3437A>T",
"hgvs_p": "p.Lys1146Met",
"transcript": "ENST00000952249.1",
"protein_id": "ENSP00000622308.1",
"transcript_support_level": null,
"aa_start": 1146,
"aa_end": null,
"aa_length": 2569,
"cds_start": 3437,
"cds_end": null,
"cds_length": 7710,
"cdna_start": 3920,
"cdna_end": null,
"cdna_length": 8948,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952249.1"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.3011A>T",
"hgvs_p": "p.Lys1004Met",
"transcript": "ENST00000952251.1",
"protein_id": "ENSP00000622310.1",
"transcript_support_level": null,
"aa_start": 1004,
"aa_end": null,
"aa_length": 2427,
"cds_start": 3011,
"cds_end": null,
"cds_length": 7284,
"cdna_start": 3260,
"cdna_end": null,
"cdna_length": 8290,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952251.1"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.2855A>T",
"hgvs_p": "p.Lys952Met",
"transcript": "ENST00000952252.1",
"protein_id": "ENSP00000622311.1",
"transcript_support_level": null,
"aa_start": 952,
"aa_end": null,
"aa_length": 2375,
"cds_start": 2855,
"cds_end": null,
"cds_length": 7128,
"cdna_start": 3104,
"cdna_end": null,
"cdna_length": 8133,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952252.1"
},
{
"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": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.2464+4806A>T",
"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.91+29801A>T",
"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": true,
"strand": true,
"consequences": [
"downstream_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.*177A>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": null,
"cds_end": null,
"cds_length": 413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 414,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000684597.1"
}
],
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"dbsnp": "rs77632596",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5816401243209839,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.569,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3533,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.14,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.293,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004369.4",
"gene_symbol": "COL6A3",
"hgnc_id": 2213,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,SD",
"hgvs_c": "c.5261A>T",
"hgvs_p": "p.Lys1754Met"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}