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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: 12-27495743-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=27495743&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 27495743,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001145010.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCO2",
"gene_hgnc_id": 34448,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Asp241Asn",
"transcript": "NM_001395208.2",
"protein_id": "NP_001382137.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 343,
"cds_start": 721,
"cds_end": null,
"cds_length": 1032,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000535986.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001395208.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCO2",
"gene_hgnc_id": 34448,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Asp241Asn",
"transcript": "ENST00000535986.2",
"protein_id": "ENSP00000441688.1",
"transcript_support_level": 5,
"aa_start": 241,
"aa_end": null,
"aa_length": 343,
"cds_start": 721,
"cds_end": null,
"cds_length": 1032,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001395208.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000535986.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCO2",
"gene_hgnc_id": 34448,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Asp241Asn",
"transcript": "NM_001145010.3",
"protein_id": "NP_001138482.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 343,
"cds_start": 721,
"cds_end": null,
"cds_length": 1032,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145010.3"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCO2",
"gene_hgnc_id": 34448,
"hgvs_c": "c.571G>A",
"hgvs_p": "p.Asp191Asn",
"transcript": "ENST00000298876.8",
"protein_id": "ENSP00000298876.4",
"transcript_support_level": 5,
"aa_start": 191,
"aa_end": null,
"aa_length": 293,
"cds_start": 571,
"cds_end": null,
"cds_length": 882,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000298876.8"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCO2",
"gene_hgnc_id": 34448,
"hgvs_c": "c.334G>A",
"hgvs_p": "p.Asp112Asn",
"transcript": "NM_001387218.3",
"protein_id": "NP_001374147.1",
"transcript_support_level": null,
"aa_start": 112,
"aa_end": null,
"aa_length": 214,
"cds_start": 334,
"cds_end": null,
"cds_length": 645,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001387218.3"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCO2",
"gene_hgnc_id": 34448,
"hgvs_c": "c.334G>A",
"hgvs_p": "p.Asp112Asn",
"transcript": "ENST00000698358.1",
"protein_id": "ENSP00000513681.1",
"transcript_support_level": null,
"aa_start": 112,
"aa_end": null,
"aa_length": 214,
"cds_start": 334,
"cds_end": null,
"cds_length": 645,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000698358.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCO2",
"gene_hgnc_id": 34448,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Asp241Asn",
"transcript": "XM_047428775.1",
"protein_id": "XP_047284731.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 343,
"cds_start": 721,
"cds_end": null,
"cds_length": 1032,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047428775.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCO2",
"gene_hgnc_id": 34448,
"hgvs_c": "c.538G>A",
"hgvs_p": "p.Asp180Asn",
"transcript": "XM_047428776.1",
"protein_id": "XP_047284732.1",
"transcript_support_level": null,
"aa_start": 180,
"aa_end": null,
"aa_length": 282,
"cds_start": 538,
"cds_end": null,
"cds_length": 849,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047428776.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCO2",
"gene_hgnc_id": 34448,
"hgvs_c": "c.484G>A",
"hgvs_p": "p.Asp162Asn",
"transcript": "XM_017019254.2",
"protein_id": "XP_016874743.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 264,
"cds_start": 484,
"cds_end": null,
"cds_length": 795,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017019254.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCO2",
"gene_hgnc_id": 34448,
"hgvs_c": "c.*36G>A",
"hgvs_p": null,
"transcript": "XM_011520636.3",
"protein_id": "XP_011518938.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 179,
"cds_start": null,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011520636.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCO2",
"gene_hgnc_id": 34448,
"hgvs_c": "n.232G>A",
"hgvs_p": null,
"transcript": "ENST00000538647.1",
"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": "ENST00000538647.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCO2",
"gene_hgnc_id": 34448,
"hgvs_c": "n.585G>A",
"hgvs_p": null,
"transcript": "ENST00000541168.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000541168.1"
}
],
"gene_symbol": "SMCO2",
"gene_hgnc_id": 34448,
"dbsnp": "rs752770562",
"frequency_reference_population": 0.0000448226,
"hom_count_reference_population": 0,
"allele_count_reference_population": 69,
"gnomad_exomes_af": 0.0000374348,
"gnomad_genomes_af": 0.000113091,
"gnomad_exomes_ac": 52,
"gnomad_genomes_ac": 17,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009059309959411621,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.032,
"revel_prediction": "Benign",
"alphamissense_score": 0.0786,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.79,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.226,
"phylop100way_prediction": "Benign",
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 6,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_001145010.3",
"gene_symbol": "SMCO2",
"hgnc_id": 34448,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Asp241Asn"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}