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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: 1-25815583-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=25815583&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Moderate",
"BP6",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "SELENON",
"hgnc_id": 15999,
"hgvs_c": "c.1638C>T",
"hgvs_p": "p.Ile546Ile",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_020451.3",
"verdict": "Likely_benign"
},
{
"benign_score": 3,
"criteria": [
"BP4_Moderate",
"BP6"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000255054",
"hgnc_id": null,
"hgvs_c": "n.123+1405C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -3,
"transcript": "ENST00000527604.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BP6,BP7",
"acmg_score": -4,
"allele_count_reference_population": 360,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.3,
"chr": "1",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Eichsfeld type congenital muscular dystrophy,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.30000001192092896,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 590,
"aa_ref": "I",
"aa_start": 546,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4314,
"cdna_start": 1676,
"cds_end": null,
"cds_length": 1773,
"cds_start": 1638,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_020451.3",
"gene_hgnc_id": 15999,
"gene_symbol": "SELENON",
"hgvs_c": "c.1638C>T",
"hgvs_p": "p.Ile546Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000361547.7",
"protein_coding": true,
"protein_id": "NP_065184.2",
"strand": true,
"transcript": "NM_020451.3",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 590,
"aa_ref": "I",
"aa_start": 546,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4314,
"cdna_start": 1676,
"cds_end": null,
"cds_length": 1773,
"cds_start": 1638,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000361547.7",
"gene_hgnc_id": 15999,
"gene_symbol": "SELENON",
"hgvs_c": "c.1638C>T",
"hgvs_p": "p.Ile546Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_020451.3",
"protein_coding": true,
"protein_id": "ENSP00000355141.2",
"strand": true,
"transcript": "ENST00000361547.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 334,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000527604.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000255054",
"hgvs_c": "n.123+1405C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000457066.1",
"strand": true,
"transcript": "ENST00000527604.1",
"transcript_support_level": 5
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 556,
"aa_ref": "I",
"aa_start": 512,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4212,
"cdna_start": 1574,
"cds_end": null,
"cds_length": 1671,
"cds_start": 1536,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_206926.2",
"gene_hgnc_id": 15999,
"gene_symbol": "SELENON",
"hgvs_c": "c.1536C>T",
"hgvs_p": "p.Ile512Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_996809.1",
"strand": true,
"transcript": "NM_206926.2",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 556,
"aa_ref": "I",
"aa_start": 512,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4212,
"cdna_start": 1574,
"cds_end": null,
"cds_length": 1671,
"cds_start": 1536,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000374315.1",
"gene_hgnc_id": 15999,
"gene_symbol": "SELENON",
"hgvs_c": "c.1536C>T",
"hgvs_p": "p.Ile512Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000363434.1",
"strand": true,
"transcript": "ENST00000374315.1",
"transcript_support_level": 5
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 533,
"aa_ref": "I",
"aa_start": 489,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1602,
"cdna_start": 1467,
"cds_end": null,
"cds_length": 1602,
"cds_start": 1467,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000354177.9",
"gene_hgnc_id": 15999,
"gene_symbol": "SELENON",
"hgvs_c": "c.1467C>T",
"hgvs_p": "p.Ile489Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000346109.5",
"strand": true,
"transcript": "ENST00000354177.9",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2032,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000494537.2",
"gene_hgnc_id": 15999,
"gene_symbol": "SELENON",
"hgvs_c": "n.*158C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000508308.1",
"strand": true,
"transcript": "ENST00000494537.2",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2032,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000494537.2",
"gene_hgnc_id": 15999,
"gene_symbol": "SELENON",
"hgvs_c": "n.*158C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000508308.1",
"strand": true,
"transcript": "ENST00000494537.2",
"transcript_support_level": 3
},
{
"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": 568,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000559265.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000255054",
"hgvs_c": "n.255+3704C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000559265.1",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs201066183",
"effect": "synonymous_variant",
"frequency_reference_population": 0.00022301958,
"gene_hgnc_id": 15999,
"gene_symbol": "SELENON",
"gnomad_exomes_ac": 334,
"gnomad_exomes_af": 0.000228478,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 26,
"gnomad_genomes_af": 0.000170651,
"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 specified|not provided|Eichsfeld type congenital muscular dystrophy",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.922,
"pos": 25815583,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_020451.3"
}
]
}