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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: 4-5576371-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=5576371&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 5576371,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000344408.10",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EVC2",
"gene_hgnc_id": 19747,
"hgvs_c": "c.3141G>A",
"hgvs_p": "p.Trp1047*",
"transcript": "NM_147127.5",
"protein_id": "NP_667338.3",
"transcript_support_level": null,
"aa_start": 1047,
"aa_end": null,
"aa_length": 1308,
"cds_start": 3141,
"cds_end": null,
"cds_length": 3927,
"cdna_start": 3187,
"cdna_end": null,
"cdna_length": 4382,
"mane_select": "ENST00000344408.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EVC2",
"gene_hgnc_id": 19747,
"hgvs_c": "c.3141G>A",
"hgvs_p": "p.Trp1047*",
"transcript": "ENST00000344408.10",
"protein_id": "ENSP00000342144.5",
"transcript_support_level": 1,
"aa_start": 1047,
"aa_end": null,
"aa_length": 1308,
"cds_start": 3141,
"cds_end": null,
"cds_length": 3927,
"cdna_start": 3187,
"cdna_end": null,
"cdna_length": 4382,
"mane_select": "NM_147127.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EVC2",
"gene_hgnc_id": 19747,
"hgvs_c": "c.2901G>A",
"hgvs_p": "p.Trp967*",
"transcript": "ENST00000310917.6",
"protein_id": "ENSP00000311683.2",
"transcript_support_level": 1,
"aa_start": 967,
"aa_end": null,
"aa_length": 1228,
"cds_start": 2901,
"cds_end": null,
"cds_length": 3687,
"cdna_start": 3633,
"cdna_end": null,
"cdna_length": 4828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EVC2",
"gene_hgnc_id": 19747,
"hgvs_c": "n.2901G>A",
"hgvs_p": null,
"transcript": "ENST00000475313.5",
"protein_id": "ENSP00000431981.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4456,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EVC2",
"gene_hgnc_id": 19747,
"hgvs_c": "n.*1534G>A",
"hgvs_p": null,
"transcript": "ENST00000509670.1",
"protein_id": "ENSP00000423876.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4079,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EVC2",
"gene_hgnc_id": 19747,
"hgvs_c": "n.*1534G>A",
"hgvs_p": null,
"transcript": "ENST00000509670.1",
"protein_id": "ENSP00000423876.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4079,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EVC2",
"gene_hgnc_id": 19747,
"hgvs_c": "c.2901G>A",
"hgvs_p": "p.Trp967*",
"transcript": "NM_001166136.2",
"protein_id": "NP_001159608.1",
"transcript_support_level": null,
"aa_start": 967,
"aa_end": null,
"aa_length": 1228,
"cds_start": 2901,
"cds_end": null,
"cds_length": 3687,
"cdna_start": 3633,
"cdna_end": null,
"cdna_length": 4828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EVC2",
"gene_hgnc_id": 19747,
"hgvs_c": "c.2901G>A",
"hgvs_p": "p.Trp967*",
"transcript": "XM_017007736.2",
"protein_id": "XP_016863225.1",
"transcript_support_level": null,
"aa_start": 967,
"aa_end": null,
"aa_length": 1228,
"cds_start": 2901,
"cds_end": null,
"cds_length": 3687,
"cdna_start": 3727,
"cdna_end": null,
"cdna_length": 4922,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EVC2",
"gene_hgnc_id": 19747,
"hgvs_c": "c.2901G>A",
"hgvs_p": "p.Trp967*",
"transcript": "XM_047449610.1",
"protein_id": "XP_047305566.1",
"transcript_support_level": null,
"aa_start": 967,
"aa_end": null,
"aa_length": 1228,
"cds_start": 2901,
"cds_end": null,
"cds_length": 3687,
"cdna_start": 3134,
"cdna_end": null,
"cdna_length": 4329,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EVC2",
"gene_hgnc_id": 19747,
"hgvs_c": "c.2901G>A",
"hgvs_p": "p.Trp967*",
"transcript": "XM_047449611.1",
"protein_id": "XP_047305567.1",
"transcript_support_level": null,
"aa_start": 967,
"aa_end": null,
"aa_length": 1165,
"cds_start": 2901,
"cds_end": null,
"cds_length": 3498,
"cdna_start": 3135,
"cdna_end": null,
"cdna_length": 9453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EVC2",
"gene_hgnc_id": 19747,
"hgvs_c": "c.3141G>A",
"hgvs_p": "p.Trp1047*",
"transcript": "XM_017007738.2",
"protein_id": "XP_016863227.1",
"transcript_support_level": null,
"aa_start": 1047,
"aa_end": null,
"aa_length": 1090,
"cds_start": 3141,
"cds_end": null,
"cds_length": 3273,
"cdna_start": 3187,
"cdna_end": null,
"cdna_length": 4481,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 19,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "EVC2",
"gene_hgnc_id": 19747,
"hgvs_c": "c.3058-1599G>A",
"hgvs_p": null,
"transcript": "XM_047449612.1",
"protein_id": "XP_047305568.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1099,
"cds_start": -4,
"cds_end": null,
"cds_length": 3300,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3387,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EVC2",
"gene_hgnc_id": 19747,
"dbsnp": "rs886037764",
"frequency_reference_population": 6.840694e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84069e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.38999998569488525,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.39,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.352,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000344408.10",
"gene_symbol": "EVC2",
"hgnc_id": 19747,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.3141G>A",
"hgvs_p": "p.Trp1047*"
}
],
"clinvar_disease": "Ellis-van Creveld syndrome,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Ellis-van Creveld syndrome|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}