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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: 18-48921591-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=48921591&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 7,
"criteria": [
"BP4_Moderate",
"BP7",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "SMAD7",
"hgnc_id": 6773,
"hgvs_c": "c.1062G>A",
"hgvs_p": "p.Thr354Thr",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -7,
"transcript": "NM_005904.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP7,BS2",
"acmg_score": -7,
"allele_count_reference_population": 90,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.42,
"chr": "18",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not provided",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.41999998688697815,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 426,
"aa_ref": "T",
"aa_start": 354,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3341,
"cdna_start": 1603,
"cds_end": null,
"cds_length": 1281,
"cds_start": 1062,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_005904.4",
"gene_hgnc_id": 6773,
"gene_symbol": "SMAD7",
"hgvs_c": "c.1062G>A",
"hgvs_p": "p.Thr354Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000262158.8",
"protein_coding": true,
"protein_id": "NP_005895.1",
"strand": false,
"transcript": "NM_005904.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 426,
"aa_ref": "T",
"aa_start": 354,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3341,
"cdna_start": 1603,
"cds_end": null,
"cds_length": 1281,
"cds_start": 1062,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000262158.8",
"gene_hgnc_id": 6773,
"gene_symbol": "SMAD7",
"hgvs_c": "c.1062G>A",
"hgvs_p": "p.Thr354Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005904.4",
"protein_coding": true,
"protein_id": "ENSP00000262158.2",
"strand": false,
"transcript": "ENST00000262158.8",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 425,
"aa_ref": "T",
"aa_start": 353,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3338,
"cdna_start": 1600,
"cds_end": null,
"cds_length": 1278,
"cds_start": 1059,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001190821.2",
"gene_hgnc_id": 6773,
"gene_symbol": "SMAD7",
"hgvs_c": "c.1059G>A",
"hgvs_p": "p.Thr353Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001177750.1",
"strand": false,
"transcript": "NM_001190821.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 425,
"aa_ref": "T",
"aa_start": 353,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1278,
"cdna_start": 1059,
"cds_end": null,
"cds_length": 1278,
"cds_start": 1059,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000589634.1",
"gene_hgnc_id": 6773,
"gene_symbol": "SMAD7",
"hgvs_c": "c.1059G>A",
"hgvs_p": "p.Thr353Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000467621.1",
"strand": false,
"transcript": "ENST00000589634.1",
"transcript_support_level": 4
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 401,
"aa_ref": "T",
"aa_start": 329,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4318,
"cdna_start": 2583,
"cds_end": null,
"cds_length": 1206,
"cds_start": 987,
"consequences": [
"synonymous_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000911789.1",
"gene_hgnc_id": 6773,
"gene_symbol": "SMAD7",
"hgvs_c": "c.987G>A",
"hgvs_p": "p.Thr329Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581848.1",
"strand": false,
"transcript": "ENST00000911789.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 383,
"aa_ref": "T",
"aa_start": 311,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4259,
"cdna_start": 2524,
"cds_end": null,
"cds_length": 1152,
"cds_start": 933,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000951831.1",
"gene_hgnc_id": 6773,
"gene_symbol": "SMAD7",
"hgvs_c": "c.933G>A",
"hgvs_p": "p.Thr311Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621890.1",
"strand": false,
"transcript": "ENST00000951831.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 238,
"aa_ref": "T",
"aa_start": 166,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2385,
"cdna_start": 647,
"cds_end": null,
"cds_length": 717,
"cds_start": 498,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001190823.2",
"gene_hgnc_id": 6773,
"gene_symbol": "SMAD7",
"hgvs_c": "c.498G>A",
"hgvs_p": "p.Thr166Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001177752.1",
"strand": false,
"transcript": "NM_001190823.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 211,
"aa_ref": "T",
"aa_start": 139,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2292,
"cdna_start": 554,
"cds_end": null,
"cds_length": 636,
"cds_start": 417,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001190822.2",
"gene_hgnc_id": 6773,
"gene_symbol": "SMAD7",
"hgvs_c": "c.417G>A",
"hgvs_p": "p.Thr139Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001177751.1",
"strand": false,
"transcript": "NM_001190822.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 211,
"aa_ref": "T",
"aa_start": 139,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1152,
"cdna_start": 554,
"cds_end": null,
"cds_length": 636,
"cds_start": 417,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000591805.5",
"gene_hgnc_id": 6773,
"gene_symbol": "SMAD7",
"hgvs_c": "c.417G>A",
"hgvs_p": "p.Thr139Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000466902.1",
"strand": false,
"transcript": "ENST00000591805.5",
"transcript_support_level": 2
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 157,
"aa_ref": "T",
"aa_start": 139,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 574,
"cdna_start": 517,
"cds_end": null,
"cds_length": 474,
"cds_start": 417,
"consequences": [
"synonymous_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000586093.1",
"gene_hgnc_id": 6773,
"gene_symbol": "SMAD7",
"hgvs_c": "c.417G>A",
"hgvs_p": "p.Thr139Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000465590.1",
"strand": false,
"transcript": "ENST00000586093.1",
"transcript_support_level": 2
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 210,
"aa_ref": "T",
"aa_start": 138,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2289,
"cdna_start": 551,
"cds_end": null,
"cds_length": 633,
"cds_start": 414,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_047437509.1",
"gene_hgnc_id": 6773,
"gene_symbol": "SMAD7",
"hgvs_c": "c.414G>A",
"hgvs_p": "p.Thr138Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047293465.1",
"strand": false,
"transcript": "XM_047437509.1",
"transcript_support_level": null
},
{
"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": 2211,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000545051.2",
"gene_hgnc_id": 6773,
"gene_symbol": "SMAD7",
"hgvs_c": "n.647G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000545051.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 563,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000585986.1",
"gene_hgnc_id": 6773,
"gene_symbol": "SMAD7",
"hgvs_c": "n.473G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000585986.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 549,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000587336.1",
"gene_hgnc_id": 6773,
"gene_symbol": "SMAD7",
"hgvs_c": "n.369G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000587336.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 401,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000588190.1",
"gene_hgnc_id": 6773,
"gene_symbol": "SMAD7",
"hgvs_c": "n.*50G>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": "ENST00000588190.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs780863704",
"effect": "synonymous_variant",
"frequency_reference_population": 0.00005576284,
"gene_hgnc_id": 6773,
"gene_symbol": "SMAD7",
"gnomad_exomes_ac": 86,
"gnomad_exomes_af": 0.0000588337,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.000026276,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.141,
"pos": 48921591,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_005904.4"
}
]
}