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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: 20-6097571-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=6097571&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PS3",
"PP5_Very_Strong"
],
"effects": [
"stop_gained"
],
"gene_symbol": "FERMT1",
"hgnc_id": 15889,
"hgvs_c": "c.910G>T",
"hgvs_p": "p.Glu304*",
"inheritance_mode": "AR",
"pathogenic_score": 20,
"score": 20,
"transcript": "NM_017671.5",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PS3,PP5_Very_Strong",
"acmg_score": 20,
"allele_count_reference_population": 201,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.63,
"chr": "20",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "FERMT1-related disorder,Kindler syndrome,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 O:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.6299999952316284,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 677,
"aa_ref": "E",
"aa_start": 304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4637,
"cdna_start": 1185,
"cds_end": null,
"cds_length": 2034,
"cds_start": 910,
"consequences": [
"stop_gained"
],
"exon_count": 15,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_017671.5",
"gene_hgnc_id": 15889,
"gene_symbol": "FERMT1",
"hgvs_c": "c.910G>T",
"hgvs_p": "p.Glu304*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000217289.9",
"protein_coding": true,
"protein_id": "NP_060141.3",
"strand": false,
"transcript": "NM_017671.5",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 677,
"aa_ref": "E",
"aa_start": 304,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4637,
"cdna_start": 1185,
"cds_end": null,
"cds_length": 2034,
"cds_start": 910,
"consequences": [
"stop_gained"
],
"exon_count": 15,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000217289.9",
"gene_hgnc_id": 15889,
"gene_symbol": "FERMT1",
"hgvs_c": "c.910G>T",
"hgvs_p": "p.Glu304*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_017671.5",
"protein_coding": true,
"protein_id": "ENSP00000217289.4",
"strand": false,
"transcript": "ENST00000217289.9",
"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": 3229,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000536936.1",
"gene_hgnc_id": 15889,
"gene_symbol": "FERMT1",
"hgvs_c": "n.*412G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000441063.2",
"strand": false,
"transcript": "ENST00000536936.1",
"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": 3229,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 14,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000536936.1",
"gene_hgnc_id": 15889,
"gene_symbol": "FERMT1",
"hgvs_c": "n.*412G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000441063.2",
"strand": false,
"transcript": "ENST00000536936.1",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 677,
"aa_ref": "E",
"aa_start": 304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7271,
"cdna_start": 4429,
"cds_end": null,
"cds_length": 2034,
"cds_start": 910,
"consequences": [
"stop_gained"
],
"exon_count": 14,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000699095.1",
"gene_hgnc_id": 15889,
"gene_symbol": "FERMT1",
"hgvs_c": "c.910G>T",
"hgvs_p": "p.Glu304*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000514127.1",
"strand": false,
"transcript": "ENST00000699095.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 677,
"aa_ref": "E",
"aa_start": 304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5254,
"cdna_start": 1802,
"cds_end": null,
"cds_length": 2034,
"cds_start": 910,
"consequences": [
"stop_gained"
],
"exon_count": 15,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000855451.1",
"gene_hgnc_id": 15889,
"gene_symbol": "FERMT1",
"hgvs_c": "c.910G>T",
"hgvs_p": "p.Glu304*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000525510.1",
"strand": false,
"transcript": "ENST00000855451.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 677,
"aa_ref": "E",
"aa_start": 304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5389,
"cdna_start": 1942,
"cds_end": null,
"cds_length": 2034,
"cds_start": 910,
"consequences": [
"stop_gained"
],
"exon_count": 15,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000855452.1",
"gene_hgnc_id": 15889,
"gene_symbol": "FERMT1",
"hgvs_c": "c.910G>T",
"hgvs_p": "p.Glu304*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000525511.1",
"strand": false,
"transcript": "ENST00000855452.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 677,
"aa_ref": "E",
"aa_start": 304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5733,
"cdna_start": 1736,
"cds_end": null,
"cds_length": 2034,
"cds_start": 910,
"consequences": [
"stop_gained"
],
"exon_count": 16,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000936598.1",
"gene_hgnc_id": 15889,
"gene_symbol": "FERMT1",
"hgvs_c": "c.910G>T",
"hgvs_p": "p.Glu304*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606657.1",
"strand": false,
"transcript": "ENST00000936598.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 677,
"aa_ref": "E",
"aa_start": 304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3582,
"cdna_start": 1931,
"cds_end": null,
"cds_length": 2034,
"cds_start": 910,
"consequences": [
"stop_gained"
],
"exon_count": 16,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000936599.1",
"gene_hgnc_id": 15889,
"gene_symbol": "FERMT1",
"hgvs_c": "c.910G>T",
"hgvs_p": "p.Glu304*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606658.1",
"strand": false,
"transcript": "ENST00000936599.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 677,
"aa_ref": "E",
"aa_start": 304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4998,
"cdna_start": 1555,
"cds_end": null,
"cds_length": 2034,
"cds_start": 910,
"consequences": [
"stop_gained"
],
"exon_count": 15,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000936600.1",
"gene_hgnc_id": 15889,
"gene_symbol": "FERMT1",
"hgvs_c": "c.910G>T",
"hgvs_p": "p.Glu304*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000606659.1",
"strand": false,
"transcript": "ENST00000936600.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 676,
"aa_ref": "E",
"aa_start": 304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4525,
"cdna_start": 1277,
"cds_end": null,
"cds_length": 2031,
"cds_start": 910,
"consequences": [
"stop_gained"
],
"exon_count": 15,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000855453.1",
"gene_hgnc_id": 15889,
"gene_symbol": "FERMT1",
"hgvs_c": "c.910G>T",
"hgvs_p": "p.Glu304*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000525512.1",
"strand": false,
"transcript": "ENST00000855453.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 677,
"aa_ref": "E",
"aa_start": 304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4640,
"cdna_start": 1188,
"cds_end": null,
"cds_length": 2034,
"cds_start": 910,
"consequences": [
"stop_gained"
],
"exon_count": 15,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_024451935.2",
"gene_hgnc_id": 15889,
"gene_symbol": "FERMT1",
"hgvs_c": "c.910G>T",
"hgvs_p": "p.Glu304*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024307703.1",
"strand": false,
"transcript": "XM_024451935.2",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 677,
"aa_ref": "E",
"aa_start": 304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4804,
"cdna_start": 1352,
"cds_end": null,
"cds_length": 2034,
"cds_start": 910,
"consequences": [
"stop_gained"
],
"exon_count": 15,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_047440259.1",
"gene_hgnc_id": 15889,
"gene_symbol": "FERMT1",
"hgvs_c": "c.910G>T",
"hgvs_p": "p.Glu304*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296215.1",
"strand": false,
"transcript": "XM_047440259.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 582,
"aa_ref": "E",
"aa_start": 209,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4300,
"cdna_start": 848,
"cds_end": null,
"cds_length": 1749,
"cds_start": 625,
"consequences": [
"stop_gained"
],
"exon_count": 14,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_047440260.1",
"gene_hgnc_id": 15889,
"gene_symbol": "FERMT1",
"hgvs_c": "c.625G>T",
"hgvs_p": "p.Glu209*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296216.1",
"strand": false,
"transcript": "XM_047440260.1",
"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": 2300,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000699096.1",
"gene_hgnc_id": 15889,
"gene_symbol": "FERMT1",
"hgvs_c": "n.1372G>T",
"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": "ENST00000699096.1",
"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": 1825,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000699097.1",
"gene_hgnc_id": 15889,
"gene_symbol": "FERMT1",
"hgvs_c": "n.80G>T",
"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": "ENST00000699097.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs146180696",
"effect": "stop_gained",
"frequency_reference_population": 0.00012453717,
"gene_hgnc_id": 15889,
"gene_symbol": "FERMT1",
"gnomad_exomes_ac": 194,
"gnomad_exomes_af": 0.00013271,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 7,
"gnomad_genomes_af": 0.0000460084,
"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": "Pathogenic",
"phenotype_combined": "Kindler syndrome|not provided|FERMT1-related disorder",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.025,
"pos": 6097571,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.15000000596046448,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.15,
"transcript": "NM_017671.5"
}
]
}