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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: 4-99608977-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=99608977&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 99608977,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000265517.10",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTTP",
"gene_hgnc_id": 7467,
"hgvs_c": "c.1769G>A",
"hgvs_p": "p.Ser590Asn",
"transcript": "NM_001386140.1",
"protein_id": "NP_001373069.1",
"transcript_support_level": null,
"aa_start": 590,
"aa_end": null,
"aa_length": 894,
"cds_start": 1769,
"cds_end": null,
"cds_length": 2685,
"cdna_start": 1855,
"cdna_end": null,
"cdna_length": 3920,
"mane_select": "ENST00000265517.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTTP",
"gene_hgnc_id": 7467,
"hgvs_c": "c.1769G>A",
"hgvs_p": "p.Ser590Asn",
"transcript": "ENST00000265517.10",
"protein_id": "ENSP00000265517.5",
"transcript_support_level": 1,
"aa_start": 590,
"aa_end": null,
"aa_length": 894,
"cds_start": 1769,
"cds_end": null,
"cds_length": 2685,
"cdna_start": 1855,
"cdna_end": null,
"cdna_length": 3920,
"mane_select": "NM_001386140.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTTP",
"gene_hgnc_id": 7467,
"hgvs_c": "c.1769G>A",
"hgvs_p": "p.Ser590Asn",
"transcript": "NM_000253.4",
"protein_id": "NP_000244.2",
"transcript_support_level": null,
"aa_start": 590,
"aa_end": null,
"aa_length": 894,
"cds_start": 1769,
"cds_end": null,
"cds_length": 2685,
"cdna_start": 1978,
"cdna_end": null,
"cdna_length": 4043,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTTP",
"gene_hgnc_id": 7467,
"hgvs_c": "c.1769G>A",
"hgvs_p": "p.Ser590Asn",
"transcript": "ENST00000457717.6",
"protein_id": "ENSP00000400821.1",
"transcript_support_level": 5,
"aa_start": 590,
"aa_end": null,
"aa_length": 894,
"cds_start": 1769,
"cds_end": null,
"cds_length": 2685,
"cdna_start": 2027,
"cdna_end": null,
"cdna_length": 3335,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTTP",
"gene_hgnc_id": 7467,
"hgvs_c": "c.1520G>A",
"hgvs_p": "p.Ser507Asn",
"transcript": "NM_001300785.2",
"protein_id": "NP_001287714.2",
"transcript_support_level": null,
"aa_start": 507,
"aa_end": null,
"aa_length": 811,
"cds_start": 1520,
"cds_end": null,
"cds_length": 2436,
"cdna_start": 1816,
"cdna_end": null,
"cdna_length": 3881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTTP",
"gene_hgnc_id": 7467,
"hgvs_c": "c.1520G>A",
"hgvs_p": "p.Ser507Asn",
"transcript": "ENST00000511045.6",
"protein_id": "ENSP00000427679.2",
"transcript_support_level": 2,
"aa_start": 507,
"aa_end": null,
"aa_length": 811,
"cds_start": 1520,
"cds_end": null,
"cds_length": 2436,
"cdna_start": 1863,
"cdna_end": null,
"cdna_length": 3154,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000248676",
"gene_hgnc_id": null,
"hgvs_c": "n.216+11910C>T",
"hgvs_p": null,
"transcript": "ENST00000508578.2",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 722,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000248676",
"gene_hgnc_id": null,
"hgvs_c": "n.214+11910C>T",
"hgvs_p": null,
"transcript": "ENST00000807449.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 673,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MTTP",
"gene_hgnc_id": 7467,
"dbsnp": "rs199422222",
"frequency_reference_population": 0.0000024863994,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000205959,
"gnomad_genomes_af": 0.00000657255,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6566998362541199,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 1,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.232,
"revel_prediction": "Benign",
"alphamissense_score": 0.4277,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.31,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.157,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.41,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": 0.999990811904691,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Strong",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PM5",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000265517.10",
"gene_symbol": "MTTP",
"hgnc_id": 7467,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1769G>A",
"hgvs_p": "p.Ser590Asn"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000807449.1",
"gene_symbol": "ENSG00000248676",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.214+11910C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}