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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: 10-110580981-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=110580981&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 110580981,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_005445.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC3",
"gene_hgnc_id": 2468,
"hgvs_c": "c.507C>T",
"hgvs_p": "p.Asp169Asp",
"transcript": "NM_005445.4",
"protein_id": "NP_005436.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 1217,
"cds_start": 507,
"cds_end": null,
"cds_length": 3654,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000361804.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005445.4"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC3",
"gene_hgnc_id": 2468,
"hgvs_c": "c.507C>T",
"hgvs_p": "p.Asp169Asp",
"transcript": "ENST00000361804.5",
"protein_id": "ENSP00000354720.5",
"transcript_support_level": 1,
"aa_start": 169,
"aa_end": null,
"aa_length": 1217,
"cds_start": 507,
"cds_end": null,
"cds_length": 3654,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005445.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361804.5"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC3",
"gene_hgnc_id": 2468,
"hgvs_c": "c.507C>T",
"hgvs_p": "p.Asp169Asp",
"transcript": "ENST00000918257.1",
"protein_id": "ENSP00000588316.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 1225,
"cds_start": 507,
"cds_end": null,
"cds_length": 3678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918257.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC3",
"gene_hgnc_id": 2468,
"hgvs_c": "c.525C>T",
"hgvs_p": "p.Asp175Asp",
"transcript": "ENST00000966376.1",
"protein_id": "ENSP00000636435.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 1223,
"cds_start": 525,
"cds_end": null,
"cds_length": 3672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000966376.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC3",
"gene_hgnc_id": 2468,
"hgvs_c": "c.507C>T",
"hgvs_p": "p.Asp169Asp",
"transcript": "ENST00000966377.1",
"protein_id": "ENSP00000636436.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 1208,
"cds_start": 507,
"cds_end": null,
"cds_length": 3627,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000966377.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC3",
"gene_hgnc_id": 2468,
"hgvs_c": "c.468C>T",
"hgvs_p": "p.Asp156Asp",
"transcript": "ENST00000918255.1",
"protein_id": "ENSP00000588314.1",
"transcript_support_level": null,
"aa_start": 156,
"aa_end": null,
"aa_length": 1204,
"cds_start": 468,
"cds_end": null,
"cds_length": 3615,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918255.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC3",
"gene_hgnc_id": 2468,
"hgvs_c": "c.507C>T",
"hgvs_p": "p.Asp169Asp",
"transcript": "ENST00000918258.1",
"protein_id": "ENSP00000588317.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 1190,
"cds_start": 507,
"cds_end": null,
"cds_length": 3573,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918258.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC3",
"gene_hgnc_id": 2468,
"hgvs_c": "c.507C>T",
"hgvs_p": "p.Asp169Asp",
"transcript": "ENST00000918256.1",
"protein_id": "ENSP00000588315.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 1082,
"cds_start": 507,
"cds_end": null,
"cds_length": 3249,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918256.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "SMC3",
"gene_hgnc_id": 2468,
"hgvs_c": "c.303+2275C>T",
"hgvs_p": null,
"transcript": "ENST00000901787.1",
"protein_id": "ENSP00000571846.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1050,
"cds_start": null,
"cds_end": null,
"cds_length": 3153,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000901787.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC3",
"gene_hgnc_id": 2468,
"hgvs_c": "n.653C>T",
"hgvs_p": null,
"transcript": "ENST00000462899.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000462899.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC3",
"gene_hgnc_id": 2468,
"hgvs_c": "n.640C>T",
"hgvs_p": null,
"transcript": "ENST00000684988.1",
"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": "retained_intron",
"feature": "ENST00000684988.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC3",
"gene_hgnc_id": 2468,
"hgvs_c": "n.421C>T",
"hgvs_p": null,
"transcript": "ENST00000687823.1",
"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": "retained_intron",
"feature": "ENST00000687823.1"
},
{
"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": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC3",
"gene_hgnc_id": 2468,
"hgvs_c": "n.2570C>T",
"hgvs_p": null,
"transcript": "ENST00000689932.1",
"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": "retained_intron",
"feature": "ENST00000689932.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC3",
"gene_hgnc_id": 2468,
"hgvs_c": "n.640C>T",
"hgvs_p": null,
"transcript": "ENST00000691297.1",
"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": "retained_intron",
"feature": "ENST00000691297.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC3",
"gene_hgnc_id": 2468,
"hgvs_c": "n.1310C>T",
"hgvs_p": null,
"transcript": "ENST00000691527.1",
"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": "retained_intron",
"feature": "ENST00000691527.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC3",
"gene_hgnc_id": 2468,
"hgvs_c": "n.626C>T",
"hgvs_p": null,
"transcript": "ENST00000692792.1",
"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": "retained_intron",
"feature": "ENST00000692792.1"
}
],
"gene_symbol": "SMC3",
"gene_hgnc_id": 2468,
"dbsnp": "rs370909218",
"frequency_reference_population": 0.000012473401,
"hom_count_reference_population": 0,
"allele_count_reference_population": 20,
"gnomad_exomes_af": 0.0000103349,
"gnomad_genomes_af": 0.0000328904,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.27000001072883606,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.27,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.871,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BS2",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_005445.4",
"gene_symbol": "SMC3",
"hgnc_id": 2468,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.507C>T",
"hgvs_p": "p.Asp169Asp"
}
],
"clinvar_disease": "Cornelia de Lange syndrome 3",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "Cornelia de Lange syndrome 3",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}