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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: 7-94427209-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=94427209&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3"
],
"effects": [
"missense_variant"
],
"gene_symbol": "COL1A2",
"hgnc_id": 2198,
"hgvs_c": "c.3181C>A",
"hgvs_p": "p.Pro1061Thr",
"inheritance_mode": "AD,AR,Unknown",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_000089.4",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3",
"acmg_score": 6,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.096,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.17,
"chr": "7",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Connective tissue disorder,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.7476374506950378,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1366,
"aa_ref": "P",
"aa_start": 1061,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5072,
"cdna_start": 3318,
"cds_end": null,
"cds_length": 4101,
"cds_start": 3181,
"consequences": [
"missense_variant"
],
"exon_count": 52,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "NM_000089.4",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.3181C>A",
"hgvs_p": "p.Pro1061Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000297268.11",
"protein_coding": true,
"protein_id": "NP_000080.2",
"strand": true,
"transcript": "NM_000089.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1366,
"aa_ref": "P",
"aa_start": 1061,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5072,
"cdna_start": 3318,
"cds_end": null,
"cds_length": 4101,
"cds_start": 3181,
"consequences": [
"missense_variant"
],
"exon_count": 52,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000297268.11",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.3181C>A",
"hgvs_p": "p.Pro1061Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000089.4",
"protein_coding": true,
"protein_id": "ENSP00000297268.6",
"strand": true,
"transcript": "ENST00000297268.11",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1365,
"aa_ref": "P",
"aa_start": 1060,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5144,
"cdna_start": 3390,
"cds_end": null,
"cds_length": 4098,
"cds_start": 3178,
"consequences": [
"missense_variant"
],
"exon_count": 52,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000959377.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.3178C>A",
"hgvs_p": "p.Pro1060Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629436.1",
"strand": true,
"transcript": "ENST00000959377.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1365,
"aa_ref": "P",
"aa_start": 1061,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4550,
"cdna_start": 3318,
"cds_end": null,
"cds_length": 4098,
"cds_start": 3181,
"consequences": [
"missense_variant"
],
"exon_count": 52,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000959379.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.3181C>A",
"hgvs_p": "p.Pro1061Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629438.1",
"strand": true,
"transcript": "ENST00000959379.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1361,
"aa_ref": "P",
"aa_start": 1056,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5005,
"cdna_start": 3259,
"cds_end": null,
"cds_length": 4086,
"cds_start": 3166,
"consequences": [
"missense_variant"
],
"exon_count": 52,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000959378.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.3166C>A",
"hgvs_p": "p.Pro1056Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629437.1",
"strand": true,
"transcript": "ENST00000959378.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1348,
"aa_ref": "P",
"aa_start": 1043,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4447,
"cdna_start": 3264,
"cds_end": null,
"cds_length": 4047,
"cds_start": 3127,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000959382.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.3127C>A",
"hgvs_p": "p.Pro1043Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629441.1",
"strand": true,
"transcript": "ENST00000959382.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1156,
"aa_ref": "P",
"aa_start": 851,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3871,
"cdna_start": 2688,
"cds_end": null,
"cds_length": 3471,
"cds_start": 2551,
"consequences": [
"missense_variant"
],
"exon_count": 43,
"exon_rank": 39,
"exon_rank_end": null,
"feature": "ENST00000959381.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.2551C>A",
"hgvs_p": "p.Pro851Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629440.1",
"strand": true,
"transcript": "ENST00000959381.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 955,
"aa_ref": "P",
"aa_start": 650,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3223,
"cdna_start": 2040,
"cds_end": null,
"cds_length": 2868,
"cds_start": 1948,
"consequences": [
"missense_variant"
],
"exon_count": 36,
"exon_rank": 32,
"exon_rank_end": null,
"feature": "ENST00000959383.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.1948C>A",
"hgvs_p": "p.Pro650Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629442.1",
"strand": true,
"transcript": "ENST00000959383.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 685,
"aa_ref": "P",
"aa_start": 380,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2465,
"cdna_start": 1231,
"cds_end": null,
"cds_length": 2058,
"cds_start": 1138,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 21,
"exon_rank_end": null,
"feature": "ENST00000959380.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "c.1138C>A",
"hgvs_p": "p.Pro380Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629439.1",
"strand": true,
"transcript": "ENST00000959380.1",
"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": 5993,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000481570.5",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "n.3631C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000481570.5",
"transcript_support_level": 2
},
{
"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": 380,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000488121.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "n.97C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000488121.1",
"transcript_support_level": 2
},
{
"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": 599,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000492110.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "n.301C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000492110.1",
"transcript_support_level": 2
},
{
"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": 1123,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000464916.1",
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"hgvs_c": "n.-103C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000464916.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1554398544",
"effect": "missense_variant",
"frequency_reference_population": 6.8408997e-7,
"gene_hgnc_id": 2198,
"gene_symbol": "COL1A2",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.8409e-7,
"gnomad_exomes_homalt": 0,
"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": "Connective tissue disorder|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.157,
"pos": 94427209,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.648,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000089.4"
}
]
}