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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: 1-99688817-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=99688817&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 99688817,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_017734.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "I",
"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": "PALMD",
"gene_hgnc_id": 15846,
"hgvs_c": "c.557C>T",
"hgvs_p": "p.Thr186Ile",
"transcript": "NM_017734.5",
"protein_id": "NP_060204.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 551,
"cds_start": 557,
"cds_end": null,
"cds_length": 1656,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000263174.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_017734.5"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": true,
"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": "PALMD",
"gene_hgnc_id": 15846,
"hgvs_c": "c.557C>T",
"hgvs_p": "p.Thr186Ile",
"transcript": "ENST00000263174.9",
"protein_id": "ENSP00000263174.4",
"transcript_support_level": 1,
"aa_start": 186,
"aa_end": null,
"aa_length": 551,
"cds_start": 557,
"cds_end": null,
"cds_length": 1656,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_017734.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000263174.9"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PALMD",
"gene_hgnc_id": 15846,
"hgvs_c": "c.557C>T",
"hgvs_p": "p.Thr186Ile",
"transcript": "ENST00000605497.5",
"protein_id": "ENSP00000473839.1",
"transcript_support_level": 1,
"aa_start": 186,
"aa_end": null,
"aa_length": 551,
"cds_start": 557,
"cds_end": null,
"cds_length": 1656,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000605497.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PALMD",
"gene_hgnc_id": 15846,
"hgvs_c": "n.3716C>T",
"hgvs_p": null,
"transcript": "ENST00000496843.1",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000496843.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"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": "PALMD",
"gene_hgnc_id": 15846,
"hgvs_c": "c.557C>T",
"hgvs_p": "p.Thr186Ile",
"transcript": "ENST00000909490.1",
"protein_id": "ENSP00000579549.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 551,
"cds_start": 557,
"cds_end": null,
"cds_length": 1656,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909490.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"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": "PALMD",
"gene_hgnc_id": 15846,
"hgvs_c": "c.557C>T",
"hgvs_p": "p.Thr186Ile",
"transcript": "ENST00000941535.1",
"protein_id": "ENSP00000611594.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 551,
"cds_start": 557,
"cds_end": null,
"cds_length": 1656,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941535.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"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": "PALMD",
"gene_hgnc_id": 15846,
"hgvs_c": "c.476C>T",
"hgvs_p": "p.Thr159Ile",
"transcript": "ENST00000941537.1",
"protein_id": "ENSP00000611596.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 524,
"cds_start": 476,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941537.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"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": "PALMD",
"gene_hgnc_id": 15846,
"hgvs_c": "c.557C>T",
"hgvs_p": "p.Thr186Ile",
"transcript": "ENST00000909491.1",
"protein_id": "ENSP00000579550.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 217,
"cds_start": 557,
"cds_end": null,
"cds_length": 654,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909491.1"
},
{
"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": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PALMD",
"gene_hgnc_id": 15846,
"hgvs_c": "c.514+1628C>T",
"hgvs_p": null,
"transcript": "ENST00000941536.1",
"protein_id": "ENSP00000611595.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 185,
"cds_start": null,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941536.1"
}
],
"gene_symbol": "PALMD",
"gene_hgnc_id": 15846,
"dbsnp": "rs145796584",
"frequency_reference_population": 0.00007147127,
"hom_count_reference_population": 0,
"allele_count_reference_population": 115,
"gnomad_exomes_af": 0.0000761937,
"gnomad_genomes_af": 0.0000262771,
"gnomad_exomes_ac": 111,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5957155227661133,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.592,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9495,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.16,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.941,
"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": 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_017734.5",
"gene_symbol": "PALMD",
"hgnc_id": 15846,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.557C>T",
"hgvs_p": "p.Thr186Ile"
}
],
"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
}