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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: 4-161385752-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=161385752&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "FSTL5",
"hgnc_id": 21386,
"hgvs_c": "c.2539G>T",
"hgvs_p": "p.Ala847Ser",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_020116.5",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000249568",
"hgnc_id": null,
"hgvs_c": "n.254-79C>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000508189.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 2,
"alphamissense_prediction": null,
"alphamissense_score": 0.0652,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.36,
"chr": "4",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.12539374828338623,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 847,
"aa_ref": "A",
"aa_start": 847,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4796,
"cdna_start": 2941,
"cds_end": null,
"cds_length": 2544,
"cds_start": 2539,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "NM_020116.5",
"gene_hgnc_id": 21386,
"gene_symbol": "FSTL5",
"hgvs_c": "c.2539G>T",
"hgvs_p": "p.Ala847Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000306100.10",
"protein_coding": true,
"protein_id": "NP_064501.2",
"strand": false,
"transcript": "NM_020116.5",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 847,
"aa_ref": "A",
"aa_start": 847,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4796,
"cdna_start": 2941,
"cds_end": null,
"cds_length": 2544,
"cds_start": 2539,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000306100.10",
"gene_hgnc_id": 21386,
"gene_symbol": "FSTL5",
"hgvs_c": "c.2539G>T",
"hgvs_p": "p.Ala847Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_020116.5",
"protein_coding": true,
"protein_id": "ENSP00000305334.4",
"strand": false,
"transcript": "ENST00000306100.10",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 846,
"aa_ref": "A",
"aa_start": 846,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4757,
"cdna_start": 2904,
"cds_end": null,
"cds_length": 2541,
"cds_start": 2536,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000379164.8",
"gene_hgnc_id": 21386,
"gene_symbol": "FSTL5",
"hgvs_c": "c.2536G>T",
"hgvs_p": "p.Ala846Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000368462.4",
"strand": false,
"transcript": "ENST00000379164.8",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 837,
"aa_ref": "A",
"aa_start": 837,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2920,
"cdna_start": 2915,
"cds_end": null,
"cds_length": 2514,
"cds_start": 2509,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000427802.2",
"gene_hgnc_id": 21386,
"gene_symbol": "FSTL5",
"hgvs_c": "c.2509G>T",
"hgvs_p": "p.Ala837Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000389270.2",
"strand": false,
"transcript": "ENST00000427802.2",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 846,
"aa_ref": "A",
"aa_start": 846,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4793,
"cdna_start": 2938,
"cds_end": null,
"cds_length": 2541,
"cds_start": 2536,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "NM_001128427.3",
"gene_hgnc_id": 21386,
"gene_symbol": "FSTL5",
"hgvs_c": "c.2536G>T",
"hgvs_p": "p.Ala846Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001121899.1",
"strand": false,
"transcript": "NM_001128427.3",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 838,
"aa_ref": "A",
"aa_start": 838,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4771,
"cdna_start": 2919,
"cds_end": null,
"cds_length": 2517,
"cds_start": 2512,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000864344.1",
"gene_hgnc_id": 21386,
"gene_symbol": "FSTL5",
"hgvs_c": "c.2512G>T",
"hgvs_p": "p.Ala838Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000534403.1",
"strand": false,
"transcript": "ENST00000864344.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 837,
"aa_ref": "A",
"aa_start": 837,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4766,
"cdna_start": 2911,
"cds_end": null,
"cds_length": 2514,
"cds_start": 2509,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NM_001128428.3",
"gene_hgnc_id": 21386,
"gene_symbol": "FSTL5",
"hgvs_c": "c.2509G>T",
"hgvs_p": "p.Ala837Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001121900.1",
"strand": false,
"transcript": "NM_001128428.3",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 838,
"aa_ref": "A",
"aa_start": 838,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4769,
"cdna_start": 2914,
"cds_end": null,
"cds_length": 2517,
"cds_start": 2512,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_011532126.1",
"gene_hgnc_id": 21386,
"gene_symbol": "FSTL5",
"hgvs_c": "c.2512G>T",
"hgvs_p": "p.Ala838Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530428.1",
"strand": false,
"transcript": "XM_011532126.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2840,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000508189.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000249568",
"hgvs_c": "n.254-79C>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000508189.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1473277955",
"effect": "missense_variant",
"frequency_reference_population": 0.000013144922,
"gene_hgnc_id": 21386,
"gene_symbol": "FSTL5",
"gnomad_exomes_ac": 0,
"gnomad_exomes_af": 0,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131449,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.55,
"pos": 161385752,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.144,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_020116.5"
}
]
}