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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: 4-169116391-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=169116391&ref=A&alt=G&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": "SH3RF1",
"hgnc_id": 17650,
"hgvs_c": "c.2017T>C",
"hgvs_p": "p.Ser673Pro",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_020870.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 12,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0793,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.49,
"chr": "4",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.19509804248809814,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 888,
"aa_ref": "S",
"aa_start": 673,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5120,
"cdna_start": 2210,
"cds_end": null,
"cds_length": 2667,
"cds_start": 2017,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_020870.4",
"gene_hgnc_id": 17650,
"gene_symbol": "SH3RF1",
"hgvs_c": "c.2017T>C",
"hgvs_p": "p.Ser673Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000284637.14",
"protein_coding": true,
"protein_id": "NP_065921.2",
"strand": false,
"transcript": "NM_020870.4",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 888,
"aa_ref": "S",
"aa_start": 673,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5120,
"cdna_start": 2210,
"cds_end": null,
"cds_length": 2667,
"cds_start": 2017,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000284637.14",
"gene_hgnc_id": 17650,
"gene_symbol": "SH3RF1",
"hgvs_c": "c.2017T>C",
"hgvs_p": "p.Ser673Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_020870.4",
"protein_coding": true,
"protein_id": "ENSP00000284637.9",
"strand": false,
"transcript": "ENST00000284637.14",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2020,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000508685.1",
"gene_hgnc_id": 17650,
"gene_symbol": "SH3RF1",
"hgvs_c": "n.1898T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000508685.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1657,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000511421.5",
"gene_hgnc_id": 17650,
"gene_symbol": "SH3RF1",
"hgvs_c": "n.*624T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000426418.1",
"strand": false,
"transcript": "ENST00000511421.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1657,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000511421.5",
"gene_hgnc_id": 17650,
"gene_symbol": "SH3RF1",
"hgvs_c": "n.*624T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000426418.1",
"strand": false,
"transcript": "ENST00000511421.5",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 908,
"aa_ref": "S",
"aa_start": 693,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5409,
"cdna_start": 2499,
"cds_end": null,
"cds_length": 2727,
"cds_start": 2077,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000924372.1",
"gene_hgnc_id": 17650,
"gene_symbol": "SH3RF1",
"hgvs_c": "c.2077T>C",
"hgvs_p": "p.Ser693Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594431.1",
"strand": false,
"transcript": "ENST00000924372.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 851,
"aa_ref": "S",
"aa_start": 636,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5214,
"cdna_start": 2304,
"cds_end": null,
"cds_length": 2556,
"cds_start": 1906,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000871180.1",
"gene_hgnc_id": 17650,
"gene_symbol": "SH3RF1",
"hgvs_c": "c.1906T>C",
"hgvs_p": "p.Ser636Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000541239.1",
"strand": false,
"transcript": "ENST00000871180.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 787,
"aa_ref": "S",
"aa_start": 572,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4871,
"cdna_start": 1963,
"cds_end": null,
"cds_length": 2364,
"cds_start": 1714,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000924373.1",
"gene_hgnc_id": 17650,
"gene_symbol": "SH3RF1",
"hgvs_c": "c.1714T>C",
"hgvs_p": "p.Ser572Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000594432.1",
"strand": false,
"transcript": "ENST00000924373.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs762395799",
"effect": "missense_variant",
"frequency_reference_population": 0.000007434806,
"gene_hgnc_id": 17650,
"gene_symbol": "SH3RF1",
"gnomad_exomes_ac": 10,
"gnomad_exomes_af": 0.0000068405,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131451,
"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": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.666,
"pos": 169116391,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.093,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_020870.4"
}
]
}