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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: 17-50077024-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=50077024&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 50077024,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_002204.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "c.1973C>G",
"hgvs_p": "p.Thr658Arg",
"transcript": "NM_002204.4",
"protein_id": "NP_002195.1",
"transcript_support_level": null,
"aa_start": 658,
"aa_end": null,
"aa_length": 1051,
"cds_start": 1973,
"cds_end": null,
"cds_length": 3156,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000320031.13",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002204.4"
},
{
"aa_ref": "T",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "c.1973C>G",
"hgvs_p": "p.Thr658Arg",
"transcript": "ENST00000320031.13",
"protein_id": "ENSP00000315190.8",
"transcript_support_level": 1,
"aa_start": 658,
"aa_end": null,
"aa_length": 1051,
"cds_start": 1973,
"cds_end": null,
"cds_length": 3156,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002204.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000320031.13"
},
{
"aa_ref": "T",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "c.1973C>G",
"hgvs_p": "p.Thr658Arg",
"transcript": "ENST00000007722.11",
"protein_id": "ENSP00000007722.7",
"transcript_support_level": 5,
"aa_start": 658,
"aa_end": null,
"aa_length": 1066,
"cds_start": 1973,
"cds_end": null,
"cds_length": 3201,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000007722.11"
},
{
"aa_ref": "T",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "c.1973C>G",
"hgvs_p": "p.Thr658Arg",
"transcript": "ENST00000876971.1",
"protein_id": "ENSP00000547030.1",
"transcript_support_level": null,
"aa_start": 658,
"aa_end": null,
"aa_length": 1051,
"cds_start": 1973,
"cds_end": null,
"cds_length": 3156,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876971.1"
},
{
"aa_ref": "T",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "c.1946C>G",
"hgvs_p": "p.Thr649Arg",
"transcript": "ENST00000876973.1",
"protein_id": "ENSP00000547032.1",
"transcript_support_level": null,
"aa_start": 649,
"aa_end": null,
"aa_length": 1042,
"cds_start": 1946,
"cds_end": null,
"cds_length": 3129,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876973.1"
},
{
"aa_ref": "T",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "c.1913C>G",
"hgvs_p": "p.Thr638Arg",
"transcript": "ENST00000876972.1",
"protein_id": "ENSP00000547031.1",
"transcript_support_level": null,
"aa_start": 638,
"aa_end": null,
"aa_length": 1031,
"cds_start": 1913,
"cds_end": null,
"cds_length": 3096,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876972.1"
},
{
"aa_ref": "T",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "c.107C>G",
"hgvs_p": "p.Thr36Arg",
"transcript": "ENST00000506827.1",
"protein_id": "ENSP00000426142.1",
"transcript_support_level": 3,
"aa_start": 36,
"aa_end": null,
"aa_length": 220,
"cds_start": 107,
"cds_end": null,
"cds_length": 663,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000506827.1"
},
{
"aa_ref": "T",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "c.1568C>G",
"hgvs_p": "p.Thr523Arg",
"transcript": "XM_005257308.3",
"protein_id": "XP_005257365.1",
"transcript_support_level": null,
"aa_start": 523,
"aa_end": null,
"aa_length": 916,
"cds_start": 1568,
"cds_end": null,
"cds_length": 2751,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005257308.3"
},
{
"aa_ref": "T",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "c.1973C>G",
"hgvs_p": "p.Thr658Arg",
"transcript": "XM_047435922.1",
"protein_id": "XP_047291878.1",
"transcript_support_level": null,
"aa_start": 658,
"aa_end": null,
"aa_length": 738,
"cds_start": 1973,
"cds_end": null,
"cds_length": 2217,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047435922.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "n.2637C>G",
"hgvs_p": null,
"transcript": "ENST00000505306.5",
"protein_id": null,
"transcript_support_level": 2,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000505306.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "n.*1366C>G",
"hgvs_p": null,
"transcript": "ENST00000506401.6",
"protein_id": "ENSP00000422826.2",
"transcript_support_level": 2,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000506401.6"
}
],
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"dbsnp": "rs540704248",
"frequency_reference_population": 0.000006573585,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000657358,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9323787689208984,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.392,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.4144,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.696,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_002204.4",
"gene_symbol": "ITGA3",
"hgnc_id": 6139,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1973C>G",
"hgvs_p": "p.Thr658Arg"
}
],
"clinvar_disease": " junctional 7, with interstitial lung disease and nephrotic syndrome,Epidermolysis bullosa,ITGA3-related disorder",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:1",
"phenotype_combined": "Epidermolysis bullosa, junctional 7, with interstitial lung disease and nephrotic syndrome|ITGA3-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}