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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: 15-66781198-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=66781198&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"PM2",
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SMAD6",
"hgnc_id": 6772,
"hgvs_c": "c.1154G>A",
"hgvs_p": "p.Ser385Asn",
"inheritance_mode": "AD,Unknown,AR",
"pathogenic_score": 2,
"score": 1,
"transcript": "NM_005585.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_score": 1,
"allele_count_reference_population": 0,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1194,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.2,
"chr": "15",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Aortic valve disease 2",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.40538516640663147,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 496,
"aa_ref": "S",
"aa_start": 385,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3828,
"cdna_start": 2177,
"cds_end": null,
"cds_length": 1491,
"cds_start": 1154,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_005585.5",
"gene_hgnc_id": 6772,
"gene_symbol": "SMAD6",
"hgvs_c": "c.1154G>A",
"hgvs_p": "p.Ser385Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000288840.10",
"protein_coding": true,
"protein_id": "NP_005576.3",
"strand": true,
"transcript": "NM_005585.5",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 496,
"aa_ref": "S",
"aa_start": 385,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3828,
"cdna_start": 2177,
"cds_end": null,
"cds_length": 1491,
"cds_start": 1154,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000288840.10",
"gene_hgnc_id": 6772,
"gene_symbol": "SMAD6",
"hgvs_c": "c.1154G>A",
"hgvs_p": "p.Ser385Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005585.5",
"protein_coding": true,
"protein_id": "ENSP00000288840.5",
"strand": true,
"transcript": "ENST00000288840.10",
"transcript_support_level": 1
},
{
"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": 1401,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000557916.5",
"gene_hgnc_id": 6772,
"gene_symbol": "SMAD6",
"hgvs_c": "n.*269G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000452955.1",
"strand": true,
"transcript": "ENST00000557916.5",
"transcript_support_level": 1
},
{
"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": 1401,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000557916.5",
"gene_hgnc_id": 6772,
"gene_symbol": "SMAD6",
"hgvs_c": "n.*269G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000452955.1",
"strand": true,
"transcript": "ENST00000557916.5",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 470,
"aa_ref": "S",
"aa_start": 359,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2788,
"cdna_start": 2001,
"cds_end": null,
"cds_length": 1413,
"cds_start": 1076,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000966143.1",
"gene_hgnc_id": 6772,
"gene_symbol": "SMAD6",
"hgvs_c": "c.1076G>A",
"hgvs_p": "p.Ser359Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000636202.1",
"strand": true,
"transcript": "ENST00000966143.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 451,
"aa_ref": "S",
"aa_start": 340,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2731,
"cdna_start": 1943,
"cds_end": null,
"cds_length": 1356,
"cds_start": 1019,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000922587.1",
"gene_hgnc_id": 6772,
"gene_symbol": "SMAD6",
"hgvs_c": "c.1019G>A",
"hgvs_p": "p.Ser340Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592646.1",
"strand": true,
"transcript": "ENST00000922587.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 235,
"aa_ref": "S",
"aa_start": 124,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6635,
"cdna_start": 4984,
"cds_end": null,
"cds_length": 708,
"cds_start": 371,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_011521561.3",
"gene_hgnc_id": 6772,
"gene_symbol": "SMAD6",
"hgvs_c": "c.371G>A",
"hgvs_p": "p.Ser124Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011519863.1",
"strand": true,
"transcript": "XM_011521561.3",
"transcript_support_level": null
},
{
"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": 573,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000559931.5",
"gene_hgnc_id": 6772,
"gene_symbol": "SMAD6",
"hgvs_c": "n.*269G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000453446.1",
"strand": true,
"transcript": "ENST00000559931.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3960,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NR_027654.2",
"gene_hgnc_id": 6772,
"gene_symbol": "SMAD6",
"hgvs_c": "n.2309G>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": "NR_027654.2",
"transcript_support_level": null
},
{
"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": 573,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000559931.5",
"gene_hgnc_id": 6772,
"gene_symbol": "SMAD6",
"hgvs_c": "n.*269G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000453446.1",
"strand": true,
"transcript": "ENST00000559931.5",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1555440093",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 6772,
"gene_symbol": "SMAD6",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"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": "Aortic valve disease 2",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.327,
"pos": 66781198,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.417,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_005585.5"
}
]
}