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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: 15-66781000-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=66781000&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 66781000,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_005585.5",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "c.956C>T",
"hgvs_p": "p.Ala319Val",
"transcript": "NM_005585.5",
"protein_id": "NP_005576.3",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 496,
"cds_start": 956,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000288840.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005585.5"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "c.956C>T",
"hgvs_p": "p.Ala319Val",
"transcript": "ENST00000288840.10",
"protein_id": "ENSP00000288840.5",
"transcript_support_level": 1,
"aa_start": 319,
"aa_end": null,
"aa_length": 496,
"cds_start": 956,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005585.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000288840.10"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "n.*71C>T",
"hgvs_p": null,
"transcript": "ENST00000557916.5",
"protein_id": "ENSP00000452955.1",
"transcript_support_level": 1,
"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": "ENST00000557916.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "n.*71C>T",
"hgvs_p": null,
"transcript": "ENST00000557916.5",
"protein_id": "ENSP00000452955.1",
"transcript_support_level": 1,
"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": "ENST00000557916.5"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "c.878C>T",
"hgvs_p": "p.Ala293Val",
"transcript": "ENST00000966143.1",
"protein_id": "ENSP00000636202.1",
"transcript_support_level": null,
"aa_start": 293,
"aa_end": null,
"aa_length": 470,
"cds_start": 878,
"cds_end": null,
"cds_length": 1413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000966143.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "c.821C>T",
"hgvs_p": "p.Ala274Val",
"transcript": "ENST00000922587.1",
"protein_id": "ENSP00000592646.1",
"transcript_support_level": null,
"aa_start": 274,
"aa_end": null,
"aa_length": 451,
"cds_start": 821,
"cds_end": null,
"cds_length": 1356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922587.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "c.173C>T",
"hgvs_p": "p.Ala58Val",
"transcript": "XM_011521561.3",
"protein_id": "XP_011519863.1",
"transcript_support_level": null,
"aa_start": 58,
"aa_end": null,
"aa_length": 235,
"cds_start": 173,
"cds_end": null,
"cds_length": 708,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011521561.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "n.*71C>T",
"hgvs_p": null,
"transcript": "ENST00000559931.5",
"protein_id": "ENSP00000453446.1",
"transcript_support_level": 3,
"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": "ENST00000559931.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "n.2111C>T",
"hgvs_p": null,
"transcript": "NR_027654.2",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "NR_027654.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"hgvs_c": "n.*71C>T",
"hgvs_p": null,
"transcript": "ENST00000559931.5",
"protein_id": "ENSP00000453446.1",
"transcript_support_level": 3,
"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": "ENST00000559931.5"
}
],
"gene_symbol": "SMAD6",
"gene_hgnc_id": 6772,
"dbsnp": "rs148705603",
"frequency_reference_population": 0.00029699347,
"hom_count_reference_population": 3,
"allele_count_reference_population": 466,
"gnomad_exomes_af": 0.000302105,
"gnomad_genomes_af": 0.000249458,
"gnomad_exomes_ac": 428,
"gnomad_genomes_ac": 38,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.014975666999816895,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.527,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1817,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.06,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.058,
"phylop100way_prediction": "Uncertain_significance",
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_005585.5",
"gene_symbol": "SMAD6",
"hgnc_id": 6772,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR,Unknown",
"hgvs_c": "c.956C>T",
"hgvs_p": "p.Ala319Val"
}
],
"clinvar_disease": "Aortic valve disease 2,Inborn genetic diseases,SMAD6-related disorder,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3",
"phenotype_combined": "Aortic valve disease 2|Inborn genetic diseases|SMAD6-related disorder|not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}