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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: 6-107883115-ACTT-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=107883115&ref=ACTT&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 9,
"criteria": [
"BP6",
"BS1",
"BS2"
],
"effects": [
"disruptive_inframe_deletion"
],
"gene_symbol": "SEC63",
"hgnc_id": 21082,
"hgvs_c": "c.1703_1705delAAG",
"hgvs_p": "p.Glu568del",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -9,
"transcript": "NM_007214.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP6,BS1,BS2",
"acmg_score": -9,
"allele_count_reference_population": 4037,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "6",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Polycystic liver disease 1,Polycystic liver disease 2,SEC63-related disorder,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2 B:1",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 760,
"aa_ref": "EV",
"aa_start": 568,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6430,
"cdna_start": 1904,
"cds_end": null,
"cds_length": 2283,
"cds_start": 1703,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 21,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_007214.5",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.1703_1705delAAG",
"hgvs_p": "p.Glu568del",
"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": "V",
"aa_end": null,
"aa_length": 760,
"aa_ref": "EV",
"aa_start": 568,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6430,
"cdna_start": 1904,
"cds_end": null,
"cds_length": 2283,
"cds_start": 1703,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 21,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000369002.9",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.1703_1705delAAG",
"hgvs_p": "p.Glu568del",
"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": "V",
"aa_end": null,
"aa_length": 789,
"aa_ref": "EV",
"aa_start": 597,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2830,
"cdna_start": 1984,
"cds_end": null,
"cds_length": 2370,
"cds_start": 1790,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 22,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000884697.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.1790_1792delAAG",
"hgvs_p": "p.Glu597del",
"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": "V",
"aa_end": null,
"aa_length": 787,
"aa_ref": "EV",
"aa_start": 595,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3495,
"cdna_start": 1986,
"cds_end": null,
"cds_length": 2364,
"cds_start": 1784,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 22,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000884696.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.1784_1786delAAG",
"hgvs_p": "p.Glu595del",
"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": "V",
"aa_end": null,
"aa_length": 786,
"aa_ref": "EV",
"aa_start": 594,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3465,
"cdna_start": 1949,
"cds_end": null,
"cds_length": 2361,
"cds_start": 1781,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 22,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000955590.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.1781_1783delAAG",
"hgvs_p": "p.Glu594del",
"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": "V",
"aa_end": null,
"aa_length": 759,
"aa_ref": "EV",
"aa_start": 567,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4511,
"cdna_start": 2002,
"cds_end": null,
"cds_length": 2280,
"cds_start": 1700,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 21,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000884693.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.1700_1702delAAG",
"hgvs_p": "p.Glu567del",
"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": "V",
"aa_end": null,
"aa_length": 743,
"aa_ref": "EV",
"aa_start": 551,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3353,
"cdna_start": 1838,
"cds_end": null,
"cds_length": 2232,
"cds_start": 1652,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 20,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000938726.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.1652_1654delAAG",
"hgvs_p": "p.Glu551del",
"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": "V",
"aa_end": null,
"aa_length": 727,
"aa_ref": "EV",
"aa_start": 568,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4292,
"cdna_start": 1904,
"cds_end": null,
"cds_length": 2184,
"cds_start": 1703,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 20,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000884694.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.1703_1705delAAG",
"hgvs_p": "p.Glu568del",
"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": "V",
"aa_end": null,
"aa_length": 702,
"aa_ref": "EV",
"aa_start": 510,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3125,
"cdna_start": 1616,
"cds_end": null,
"cds_length": 2109,
"cds_start": 1529,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 20,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000938728.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.1529_1531delAAG",
"hgvs_p": "p.Glu510del",
"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": "V",
"aa_end": null,
"aa_length": 684,
"aa_ref": "EV",
"aa_start": 492,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3114,
"cdna_start": 1598,
"cds_end": null,
"cds_length": 2055,
"cds_start": 1475,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 19,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000955591.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.1475_1477delAAG",
"hgvs_p": "p.Glu492del",
"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": "V",
"aa_end": null,
"aa_length": 410,
"aa_ref": "EV",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2323,
"cdna_start": 807,
"cds_end": null,
"cds_length": 1233,
"cds_start": 653,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000938727.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.653_655delAAG",
"hgvs_p": "p.Glu218del",
"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": "V",
"aa_end": null,
"aa_length": 704,
"aa_ref": "EV",
"aa_start": 512,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7406,
"cdna_start": 2880,
"cds_end": null,
"cds_length": 2115,
"cds_start": 1535,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 21,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "XM_047418130.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.1535_1537delAAG",
"hgvs_p": "p.Glu512del",
"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": "V",
"aa_end": null,
"aa_length": 620,
"aa_ref": "EV",
"aa_start": 428,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6330,
"cdna_start": 1804,
"cds_end": null,
"cds_length": 1863,
"cds_start": 1283,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 20,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_047418131.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.1283_1285delAAG",
"hgvs_p": "p.Glu428del",
"intron_rank": null,
"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": 673,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3672,
"cdna_start": null,
"cds_end": null,
"cds_length": 2022,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000884695.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "c.1675-6456_1675-6454delAAG",
"hgvs_p": null,
"intron_rank": 16,
"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": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 709,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000473746.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "n.350_352delAAG",
"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": "ENST00000473746.1",
"transcript_support_level": 2
},
{
"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": 416,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000465210.1",
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"hgvs_c": "n.-6_-4delAAG",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000465210.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs752018806",
"effect": "disruptive_inframe_deletion",
"frequency_reference_population": 0.0025039664,
"gene_hgnc_id": 21082,
"gene_symbol": "SEC63",
"gnomad_exomes_ac": 3640,
"gnomad_exomes_af": 0.00249318,
"gnomad_exomes_homalt": 16,
"gnomad_genomes_ac": 397,
"gnomad_genomes_af": 0.00260735,
"gnomad_genomes_homalt": 5,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 21,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Polycystic liver disease 2|Polycystic liver disease 1|not provided|SEC63-related disorder",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.333,
"pos": 107883115,
"ref": "ACTT",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_007214.5"
}
]
}