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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: 19-6380574-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=6380574&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS2"
],
"effects": [
"missense_variant",
"splice_region_variant"
],
"gene_symbol": "GTF2F1",
"hgnc_id": 4652,
"hgvs_c": "c.1348G>C",
"hgvs_p": "p.Gly450Arg",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_002096.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_score": -6,
"allele_count_reference_population": 7,
"alphamissense_prediction": null,
"alphamissense_score": 0.5794,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.58,
"chr": "19",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.21927502751350403,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 517,
"aa_ref": "G",
"aa_start": 450,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2432,
"cdna_start": 1517,
"cds_end": null,
"cds_length": 1554,
"cds_start": 1348,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_002096.3",
"gene_hgnc_id": 4652,
"gene_symbol": "GTF2F1",
"hgvs_c": "c.1348G>C",
"hgvs_p": "p.Gly450Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000394456.10",
"protein_coding": true,
"protein_id": "NP_002087.2",
"strand": false,
"transcript": "NM_002096.3",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 517,
"aa_ref": "G",
"aa_start": 450,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2432,
"cdna_start": 1517,
"cds_end": null,
"cds_length": 1554,
"cds_start": 1348,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000394456.10",
"gene_hgnc_id": 4652,
"gene_symbol": "GTF2F1",
"hgvs_c": "c.1348G>C",
"hgvs_p": "p.Gly450Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002096.3",
"protein_coding": true,
"protein_id": "ENSP00000377969.3",
"strand": false,
"transcript": "ENST00000394456.10",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 516,
"aa_ref": "G",
"aa_start": 449,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2406,
"cdna_start": 1514,
"cds_end": null,
"cds_length": 1551,
"cds_start": 1345,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000869875.1",
"gene_hgnc_id": 4652,
"gene_symbol": "GTF2F1",
"hgvs_c": "c.1345G>C",
"hgvs_p": "p.Gly449Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000539934.1",
"strand": false,
"transcript": "ENST00000869875.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 515,
"aa_ref": "G",
"aa_start": 448,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2426,
"cdna_start": 1511,
"cds_end": null,
"cds_length": 1548,
"cds_start": 1342,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000933129.1",
"gene_hgnc_id": 4652,
"gene_symbol": "GTF2F1",
"hgvs_c": "c.1342G>C",
"hgvs_p": "p.Gly448Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603188.1",
"strand": false,
"transcript": "ENST00000933129.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 508,
"aa_ref": "G",
"aa_start": 441,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1802,
"cdna_start": 1490,
"cds_end": null,
"cds_length": 1527,
"cds_start": 1321,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000933130.1",
"gene_hgnc_id": 4652,
"gene_symbol": "GTF2F1",
"hgvs_c": "c.1321G>C",
"hgvs_p": "p.Gly441Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603189.1",
"strand": false,
"transcript": "ENST00000933130.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 433,
"aa_ref": "G",
"aa_start": 366,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1705,
"cdna_start": 1096,
"cds_end": null,
"cds_length": 1302,
"cds_start": 1096,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000593678.5",
"gene_hgnc_id": 4652,
"gene_symbol": "GTF2F1",
"hgvs_c": "c.1096G>C",
"hgvs_p": "p.Gly366Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000469091.1",
"strand": false,
"transcript": "ENST00000593678.5",
"transcript_support_level": 2
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 526,
"aa_ref": "G",
"aa_start": 459,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2414,
"cdna_start": 1499,
"cds_end": null,
"cds_length": 1581,
"cds_start": 1375,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_047438710.1",
"gene_hgnc_id": 4652,
"gene_symbol": "GTF2F1",
"hgvs_c": "c.1375G>C",
"hgvs_p": "p.Gly459Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047294666.1",
"strand": false,
"transcript": "XM_047438710.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1002,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000594213.5",
"gene_hgnc_id": 4652,
"gene_symbol": "GTF2F1",
"hgvs_c": "n.715G>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": "ENST00000594213.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 762,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000594965.1",
"gene_hgnc_id": 4652,
"gene_symbol": "GTF2F1",
"hgvs_c": "n.666G>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": "ENST00000594965.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.000141068847235366,
"dbsnp": "rs756438444",
"effect": "missense_variant,splice_region_variant",
"frequency_reference_population": 0.000004789154,
"gene_hgnc_id": 4652,
"gene_symbol": "GTF2F1",
"gnomad_exomes_ac": 7,
"gnomad_exomes_af": 0.00000478915,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"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": 2.166,
"pos": 6380574,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.138,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_002096.3"
}
]
}