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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: 6-109443325-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=109443325&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 109443325,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_003080.3",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD2",
"gene_hgnc_id": 11121,
"hgvs_c": "c.788C>T",
"hgvs_p": "p.Pro263Leu",
"transcript": "NM_003080.3",
"protein_id": "NP_003071.2",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 423,
"cds_start": 788,
"cds_end": null,
"cds_length": 1272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000258052.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003080.3"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD2",
"gene_hgnc_id": 11121,
"hgvs_c": "c.788C>T",
"hgvs_p": "p.Pro263Leu",
"transcript": "ENST00000258052.8",
"protein_id": "ENSP00000258052.3",
"transcript_support_level": 1,
"aa_start": 263,
"aa_end": null,
"aa_length": 423,
"cds_start": 788,
"cds_end": null,
"cds_length": 1272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003080.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000258052.8"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD2",
"gene_hgnc_id": 11121,
"hgvs_c": "c.770C>T",
"hgvs_p": "p.Pro257Leu",
"transcript": "ENST00000882802.1",
"protein_id": "ENSP00000552861.1",
"transcript_support_level": null,
"aa_start": 257,
"aa_end": null,
"aa_length": 417,
"cds_start": 770,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882802.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"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": "SMPD2",
"gene_hgnc_id": 11121,
"hgvs_c": "c.698C>T",
"hgvs_p": "p.Pro233Leu",
"transcript": "ENST00000882801.1",
"protein_id": "ENSP00000552860.1",
"transcript_support_level": null,
"aa_start": 233,
"aa_end": null,
"aa_length": 393,
"cds_start": 698,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882801.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD2",
"gene_hgnc_id": 11121,
"hgvs_c": "c.476C>T",
"hgvs_p": "p.Pro159Leu",
"transcript": "ENST00000458487.1",
"protein_id": "ENSP00000399731.1",
"transcript_support_level": 2,
"aa_start": 159,
"aa_end": null,
"aa_length": 202,
"cds_start": 476,
"cds_end": null,
"cds_length": 611,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000458487.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"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": "SMPD2",
"gene_hgnc_id": 11121,
"hgvs_c": "c.473C>T",
"hgvs_p": "p.Pro158Leu",
"transcript": "XM_011536079.2",
"protein_id": "XP_011534381.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 318,
"cds_start": 473,
"cds_end": null,
"cds_length": 957,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011536079.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SMPD2",
"gene_hgnc_id": 11121,
"hgvs_c": "n.1128-7C>T",
"hgvs_p": null,
"transcript": "XR_942566.3",
"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": "XR_942566.3"
}
],
"gene_symbol": "SMPD2",
"gene_hgnc_id": 11121,
"dbsnp": "rs766849769",
"frequency_reference_population": 0.000029741066,
"hom_count_reference_population": 0,
"allele_count_reference_population": 48,
"gnomad_exomes_af": 0.0000301018,
"gnomad_genomes_af": 0.0000262774,
"gnomad_exomes_ac": 44,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.42656195163726807,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10999999940395355,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.534,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0923,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.17,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.806,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.11,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_003080.3",
"gene_symbol": "SMPD2",
"hgnc_id": 11121,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.788C>T",
"hgvs_p": "p.Pro263Leu"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}