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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: 5-172338628-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=172338628&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 172338628,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001017995.3",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2B",
"gene_hgnc_id": 29242,
"hgvs_c": "c.2477C>T",
"hgvs_p": "p.Pro826Leu",
"transcript": "NM_001017995.3",
"protein_id": "NP_001017995.1",
"transcript_support_level": null,
"aa_start": 826,
"aa_end": null,
"aa_length": 911,
"cds_start": 2477,
"cds_end": null,
"cds_length": 2736,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000311601.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001017995.3"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2B",
"gene_hgnc_id": 29242,
"hgvs_c": "c.2477C>T",
"hgvs_p": "p.Pro826Leu",
"transcript": "ENST00000311601.6",
"protein_id": "ENSP00000309714.5",
"transcript_support_level": 1,
"aa_start": 826,
"aa_end": null,
"aa_length": 911,
"cds_start": 2477,
"cds_end": null,
"cds_length": 2736,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001017995.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000311601.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2B",
"gene_hgnc_id": 29242,
"hgvs_c": "c.1188+7508C>T",
"hgvs_p": null,
"transcript": "ENST00000519643.5",
"protein_id": "ENSP00000430890.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 430,
"cds_start": null,
"cds_end": null,
"cds_length": 1293,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000519643.5"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2B",
"gene_hgnc_id": 29242,
"hgvs_c": "c.2579C>T",
"hgvs_p": "p.Pro860Leu",
"transcript": "ENST00000918640.1",
"protein_id": "ENSP00000588699.1",
"transcript_support_level": null,
"aa_start": 860,
"aa_end": null,
"aa_length": 945,
"cds_start": 2579,
"cds_end": null,
"cds_length": 2838,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918640.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2B",
"gene_hgnc_id": 29242,
"hgvs_c": "c.2561C>T",
"hgvs_p": "p.Pro854Leu",
"transcript": "ENST00000971124.1",
"protein_id": "ENSP00000641183.1",
"transcript_support_level": null,
"aa_start": 854,
"aa_end": null,
"aa_length": 939,
"cds_start": 2561,
"cds_end": null,
"cds_length": 2820,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971124.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2B",
"gene_hgnc_id": 29242,
"hgvs_c": "c.2429C>T",
"hgvs_p": "p.Pro810Leu",
"transcript": "ENST00000918641.1",
"protein_id": "ENSP00000588700.1",
"transcript_support_level": null,
"aa_start": 810,
"aa_end": null,
"aa_length": 895,
"cds_start": 2429,
"cds_end": null,
"cds_length": 2688,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918641.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2B",
"gene_hgnc_id": 29242,
"hgvs_c": "c.2561C>T",
"hgvs_p": "p.Pro854Leu",
"transcript": "XM_017009351.2",
"protein_id": "XP_016864840.1",
"transcript_support_level": null,
"aa_start": 854,
"aa_end": null,
"aa_length": 939,
"cds_start": 2561,
"cds_end": null,
"cds_length": 2820,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017009351.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2B",
"gene_hgnc_id": 29242,
"hgvs_c": "c.1227+7508C>T",
"hgvs_p": null,
"transcript": "ENST00000636523.1",
"protein_id": "ENSP00000490082.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 443,
"cds_start": null,
"cds_end": null,
"cds_length": 1332,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000636523.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2B",
"gene_hgnc_id": 29242,
"hgvs_c": "c.1188+7508C>T",
"hgvs_p": null,
"transcript": "NM_001308175.2",
"protein_id": "NP_001295104.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 430,
"cds_start": null,
"cds_end": null,
"cds_length": 1293,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001308175.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SH3PXD2B",
"gene_hgnc_id": 29242,
"hgvs_c": "c.199-4859C>T",
"hgvs_p": null,
"transcript": "ENST00000518522.5",
"protein_id": "ENSP00000428076.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 80,
"cds_start": null,
"cds_end": null,
"cds_length": 243,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000518522.5"
}
],
"gene_symbol": "SH3PXD2B",
"gene_hgnc_id": 29242,
"dbsnp": "rs73317796",
"frequency_reference_population": 0.0018213628,
"hom_count_reference_population": 56,
"allele_count_reference_population": 2940,
"gnomad_exomes_af": 0.000983692,
"gnomad_genomes_af": 0.00985978,
"gnomad_exomes_ac": 1438,
"gnomad_genomes_ac": 1502,
"gnomad_exomes_homalt": 30,
"gnomad_genomes_homalt": 26,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0027823448181152344,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.085,
"revel_prediction": "Benign",
"alphamissense_score": 0.0688,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.207,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001017995.3",
"gene_symbol": "SH3PXD2B",
"hgnc_id": 29242,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2477C>T",
"hgvs_p": "p.Pro826Leu"
}
],
"clinvar_disease": "Frank-Ter Haar syndrome,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:1",
"phenotype_combined": "Frank-Ter Haar syndrome|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}