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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: 1-109738312-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=109738312&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 109738312,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000849.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GSTM3",
"gene_hgnc_id": 4635,
"hgvs_c": "c.244C>A",
"hgvs_p": "p.Arg82Ser",
"transcript": "NM_000849.5",
"protein_id": "NP_000840.2",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 225,
"cds_start": 244,
"cds_end": null,
"cds_length": 678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000361066.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000849.5"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GSTM3",
"gene_hgnc_id": 4635,
"hgvs_c": "c.244C>A",
"hgvs_p": "p.Arg82Ser",
"transcript": "ENST00000361066.7",
"protein_id": "ENSP00000354357.2",
"transcript_support_level": 1,
"aa_start": 82,
"aa_end": null,
"aa_length": 225,
"cds_start": 244,
"cds_end": null,
"cds_length": 678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000849.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361066.7"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GSTM3",
"gene_hgnc_id": 4635,
"hgvs_c": "c.244C>A",
"hgvs_p": "p.Arg82Ser",
"transcript": "ENST00000256594.7",
"protein_id": "ENSP00000256594.3",
"transcript_support_level": 1,
"aa_start": 82,
"aa_end": null,
"aa_length": 225,
"cds_start": 244,
"cds_end": null,
"cds_length": 678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000256594.7"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GSTM3",
"gene_hgnc_id": 4635,
"hgvs_c": "c.493C>A",
"hgvs_p": "p.Arg165Ser",
"transcript": "ENST00000872817.1",
"protein_id": "ENSP00000542876.1",
"transcript_support_level": null,
"aa_start": 165,
"aa_end": null,
"aa_length": 308,
"cds_start": 493,
"cds_end": null,
"cds_length": 927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000872817.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GSTM3",
"gene_hgnc_id": 4635,
"hgvs_c": "c.244C>A",
"hgvs_p": "p.Arg82Ser",
"transcript": "ENST00000944483.1",
"protein_id": "ENSP00000614542.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 228,
"cds_start": 244,
"cds_end": null,
"cds_length": 687,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944483.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GSTM3",
"gene_hgnc_id": 4635,
"hgvs_c": "n.208C>A",
"hgvs_p": null,
"transcript": "ENST00000486823.5",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000486823.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GSTM3",
"gene_hgnc_id": 4635,
"hgvs_c": "n.589C>A",
"hgvs_p": null,
"transcript": "ENST00000488824.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000488824.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GSTM3",
"gene_hgnc_id": 4635,
"hgvs_c": "n.478C>A",
"hgvs_p": null,
"transcript": "NR_024537.2",
"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": "NR_024537.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GSTM5",
"gene_hgnc_id": 4637,
"hgvs_c": "n.82+25964G>T",
"hgvs_p": null,
"transcript": "ENST00000429410.2",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000429410.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000241720",
"gene_hgnc_id": null,
"hgvs_c": "n.627+1171G>T",
"hgvs_p": null,
"transcript": "ENST00000431955.1",
"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": "pseudogene",
"feature": "ENST00000431955.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GSTM3",
"gene_hgnc_id": 4635,
"hgvs_c": "n.-169C>A",
"hgvs_p": null,
"transcript": "ENST00000476321.5",
"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": "pseudogene",
"feature": "ENST00000476321.5"
}
],
"gene_symbol": "GSTM3",
"gene_hgnc_id": 4635,
"dbsnp": "rs779672621",
"frequency_reference_population": 6.8416955e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.8417e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8902921080589294,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.547,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9901,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.09,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.211,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000849.5",
"gene_symbol": "GSTM3",
"hgnc_id": 4635,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.244C>A",
"hgvs_p": "p.Arg82Ser"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000429410.2",
"gene_symbol": "GSTM5",
"hgnc_id": 4637,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.82+25964G>T",
"hgvs_p": null
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000431955.1",
"gene_symbol": "ENSG00000241720",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.627+1171G>T",
"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
}