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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: 6-107929466-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=107929466&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"effects": [
"stop_gained"
],
"gene_symbol": "SEC63",
"hgnc_id": 21082,
"hgvs_c": "c.173G>A",
"hgvs_p": "p.Trp58*",
"inheritance_mode": "AD",
"pathogenic_score": 11,
"score": 11,
"transcript": "NM_007214.5",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_score": 11,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.65,
"chr": "6",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Polycystic liver disease 2",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.6499999761581421,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 760,
"aa_ref": "W",
"aa_start": 58,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6430,
"cdna_start": 372,
"cds_end": null,
"cds_length": 2283,
"cds_start": 173,
"consequences": [
"stop_gained"
],
"exon_count": 21,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_007214.5",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.173G>A",
"hgvs_p": "p.Trp58*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000369002.9",
"protein_coding": true,
"protein_id": "NP_009145.1",
"strand": false,
"transcript": "NM_007214.5",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 760,
"aa_ref": "W",
"aa_start": 58,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6430,
"cdna_start": 372,
"cds_end": null,
"cds_length": 2283,
"cds_start": 173,
"consequences": [
"stop_gained"
],
"exon_count": 21,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000369002.9",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.173G>A",
"hgvs_p": "p.Trp58*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_007214.5",
"protein_coding": true,
"protein_id": "ENSP00000357998.4",
"strand": false,
"transcript": "ENST00000369002.9",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 789,
"aa_ref": "W",
"aa_start": 58,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2830,
"cdna_start": 365,
"cds_end": null,
"cds_length": 2370,
"cds_start": 173,
"consequences": [
"stop_gained"
],
"exon_count": 22,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000884697.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.173G>A",
"hgvs_p": "p.Trp58*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000554756.1",
"strand": false,
"transcript": "ENST00000884697.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 787,
"aa_ref": "W",
"aa_start": 58,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3495,
"cdna_start": 373,
"cds_end": null,
"cds_length": 2364,
"cds_start": 173,
"consequences": [
"stop_gained"
],
"exon_count": 22,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000884696.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.173G>A",
"hgvs_p": "p.Trp58*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000554755.1",
"strand": false,
"transcript": "ENST00000884696.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 786,
"aa_ref": "W",
"aa_start": 58,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3465,
"cdna_start": 339,
"cds_end": null,
"cds_length": 2361,
"cds_start": 173,
"consequences": [
"stop_gained"
],
"exon_count": 22,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000955590.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.173G>A",
"hgvs_p": "p.Trp58*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625649.1",
"strand": false,
"transcript": "ENST00000955590.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 759,
"aa_ref": "W",
"aa_start": 58,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4511,
"cdna_start": 473,
"cds_end": null,
"cds_length": 2280,
"cds_start": 173,
"consequences": [
"stop_gained"
],
"exon_count": 21,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000884693.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.173G>A",
"hgvs_p": "p.Trp58*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000554752.1",
"strand": false,
"transcript": "ENST00000884693.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 743,
"aa_ref": "W",
"aa_start": 58,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3353,
"cdna_start": 357,
"cds_end": null,
"cds_length": 2232,
"cds_start": 173,
"consequences": [
"stop_gained"
],
"exon_count": 20,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000938726.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.173G>A",
"hgvs_p": "p.Trp58*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000608785.1",
"strand": false,
"transcript": "ENST00000938726.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 727,
"aa_ref": "W",
"aa_start": 58,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4292,
"cdna_start": 372,
"cds_end": null,
"cds_length": 2184,
"cds_start": 173,
"consequences": [
"stop_gained"
],
"exon_count": 20,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000884694.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.173G>A",
"hgvs_p": "p.Trp58*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000554753.1",
"strand": false,
"transcript": "ENST00000884694.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 702,
"aa_ref": "W",
"aa_start": 58,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3125,
"cdna_start": 258,
"cds_end": null,
"cds_length": 2109,
"cds_start": 173,
"consequences": [
"stop_gained"
],
"exon_count": 20,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000938728.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.173G>A",
"hgvs_p": "p.Trp58*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000608787.1",
"strand": false,
"transcript": "ENST00000938728.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 684,
"aa_ref": "W",
"aa_start": 58,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3114,
"cdna_start": 294,
"cds_end": null,
"cds_length": 2055,
"cds_start": 173,
"consequences": [
"stop_gained"
],
"exon_count": 19,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000955591.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.173G>A",
"hgvs_p": "p.Trp58*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625650.1",
"strand": false,
"transcript": "ENST00000955591.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 673,
"aa_ref": "W",
"aa_start": 58,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3672,
"cdna_start": 431,
"cds_end": null,
"cds_length": 2022,
"cds_start": 173,
"consequences": [
"stop_gained"
],
"exon_count": 19,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000884695.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.173G>A",
"hgvs_p": "p.Trp58*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000554754.1",
"strand": false,
"transcript": "ENST00000884695.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 410,
"aa_ref": "W",
"aa_start": 58,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2323,
"cdna_start": 325,
"cds_end": null,
"cds_length": 1233,
"cds_start": 173,
"consequences": [
"stop_gained"
],
"exon_count": 12,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000938727.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.173G>A",
"hgvs_p": "p.Trp58*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000608786.1",
"strand": false,
"transcript": "ENST00000938727.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 160,
"aa_ref": "W",
"aa_start": 2,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 647,
"cdna_start": 168,
"cds_end": null,
"cds_length": 484,
"cds_start": 5,
"consequences": [
"stop_gained"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000429168.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.5G>A",
"hgvs_p": "p.Trp2*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000403144.1",
"strand": false,
"transcript": "ENST00000429168.1",
"transcript_support_level": 5
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 704,
"aa_ref": "W",
"aa_start": 2,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7406,
"cdna_start": 1348,
"cds_end": null,
"cds_length": 2115,
"cds_start": 5,
"consequences": [
"stop_gained"
],
"exon_count": 21,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_047418130.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.5G>A",
"hgvs_p": "p.Trp2*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047274086.1",
"strand": false,
"transcript": "XM_047418130.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 620,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6330,
"cdna_start": null,
"cds_end": null,
"cds_length": 1863,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 20,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047418131.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.-196-4534G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047274087.1",
"strand": false,
"transcript": "XM_047418131.1",
"transcript_support_level": null
},
{
"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": 583,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000446496.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "n.*72G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000410968.1",
"strand": false,
"transcript": "ENST00000446496.1",
"transcript_support_level": 4
},
{
"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": 724,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000484803.5",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "n.95G>A",
"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": "ENST00000484803.5",
"transcript_support_level": 2
},
{
"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": 583,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000446496.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "n.*72G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000410968.1",
"strand": false,
"transcript": "ENST00000446496.1",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs119103233",
"effect": "stop_gained",
"frequency_reference_population": 0.0000065751406,
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"gnomad_exomes_ac": 0,
"gnomad_exomes_af": 0,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657514,
"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": "Polycystic liver disease 2",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.455,
"pos": 107929466,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_007214.5"
}
]
}