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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: 6-122801319-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=122801319&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 122801319,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_006714.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPDL3A",
"gene_hgnc_id": 17389,
"hgvs_c": "c.481C>T",
"hgvs_p": "p.Pro161Ser",
"transcript": "NM_006714.5",
"protein_id": "NP_006705.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 453,
"cds_start": 481,
"cds_end": null,
"cds_length": 1362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000368440.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006714.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPDL3A",
"gene_hgnc_id": 17389,
"hgvs_c": "c.481C>T",
"hgvs_p": "p.Pro161Ser",
"transcript": "ENST00000368440.5",
"protein_id": "ENSP00000357425.4",
"transcript_support_level": 1,
"aa_start": 161,
"aa_end": null,
"aa_length": 453,
"cds_start": 481,
"cds_end": null,
"cds_length": 1362,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006714.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000368440.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPDL3A",
"gene_hgnc_id": 17389,
"hgvs_c": "c.481C>T",
"hgvs_p": "p.Pro161Ser",
"transcript": "ENST00000894535.1",
"protein_id": "ENSP00000564594.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 336,
"cds_start": 481,
"cds_end": null,
"cds_length": 1011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000894535.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPDL3A",
"gene_hgnc_id": 17389,
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Pro30Ser",
"transcript": "NM_001286138.2",
"protein_id": "NP_001273067.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 322,
"cds_start": 88,
"cds_end": null,
"cds_length": 969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001286138.2"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPDL3A",
"gene_hgnc_id": 17389,
"hgvs_c": "c.88C>T",
"hgvs_p": "p.Pro30Ser",
"transcript": "ENST00000539041.5",
"protein_id": "ENSP00000442152.1",
"transcript_support_level": 2,
"aa_start": 30,
"aa_end": null,
"aa_length": 322,
"cds_start": 88,
"cds_end": null,
"cds_length": 969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000539041.5"
},
{
"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": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SMPDL3A",
"gene_hgnc_id": 17389,
"hgvs_c": "c.472-2362C>T",
"hgvs_p": null,
"transcript": "ENST00000894537.1",
"protein_id": "ENSP00000564596.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 415,
"cds_start": null,
"cds_end": null,
"cds_length": 1248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000894537.1"
},
{
"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": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SMPDL3A",
"gene_hgnc_id": 17389,
"hgvs_c": "c.472-3590C>T",
"hgvs_p": null,
"transcript": "ENST00000894534.1",
"protein_id": "ENSP00000564593.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 364,
"cds_start": null,
"cds_end": null,
"cds_length": 1095,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000894534.1"
},
{
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SMPDL3A",
"gene_hgnc_id": 17389,
"hgvs_c": "c.113-2345C>T",
"hgvs_p": null,
"transcript": "ENST00000894536.1",
"protein_id": "ENSP00000564595.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 301,
"cds_start": null,
"cds_end": null,
"cds_length": 906,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000894536.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000294893",
"gene_hgnc_id": null,
"hgvs_c": "n.331-19982G>A",
"hgvs_p": null,
"transcript": "ENST00000726593.1",
"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": "pseudogene",
"feature": "ENST00000726593.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000294893",
"gene_hgnc_id": null,
"hgvs_c": "n.314+12984G>A",
"hgvs_p": null,
"transcript": "ENST00000726594.1",
"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": "pseudogene",
"feature": "ENST00000726594.1"
}
],
"gene_symbol": "SMPDL3A",
"gene_hgnc_id": 17389,
"dbsnp": "rs28385609",
"frequency_reference_population": 0.1362394,
"hom_count_reference_population": 16747,
"allele_count_reference_population": 218913,
"gnomad_exomes_af": 0.138743,
"gnomad_genomes_af": 0.112319,
"gnomad_exomes_ac": 201814,
"gnomad_genomes_ac": 17099,
"gnomad_exomes_homalt": 15589,
"gnomad_genomes_homalt": 1158,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0019767582416534424,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.11999999731779099,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.431,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5156,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.04,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.57,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.12,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_006714.5",
"gene_symbol": "SMPDL3A",
"hgnc_id": 17389,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.481C>T",
"hgvs_p": "p.Pro161Ser"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000726593.1",
"gene_symbol": "ENSG00000294893",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.331-19982G>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}