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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: X-155071541-TGGTGCAGGC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=155071541&ref=TGGTGCAGGC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"PM4",
"PP3",
"BP6_Moderate",
"BS2"
],
"effects": [
"disruptive_inframe_deletion"
],
"gene_symbol": "BRCC3",
"hgnc_id": 24185,
"hgvs_c": "c.27_35delGCAGGCGGT",
"hgvs_p": "p.Gln10_Val12del",
"inheritance_mode": "XL,AD",
"pathogenic_score": 3,
"score": -3,
"transcript": "NM_024332.4",
"verdict": "Likely_benign"
},
{
"benign_score": 6,
"criteria": [
"PP3",
"BP6_Moderate",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "MTCP1",
"hgnc_id": 7423,
"hgvs_c": "c.-47-5493_-47-5485delGCCTGCACC",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 1,
"score": -5,
"transcript": "ENST00000362018.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM4,PP3,BP6_Moderate,BS2",
"acmg_score": -3,
"allele_count_reference_population": 710,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "X",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 291,
"aa_ref": "VQAV",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2769,
"cdna_start": 47,
"cds_end": null,
"cds_length": 876,
"cds_start": 27,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 11,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001018055.3",
"gene_hgnc_id": 24185,
"gene_symbol": "BRCC3",
"hgvs_c": "c.27_35delGCAGGCGGT",
"hgvs_p": "p.Gln10_Val12del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000330045.12",
"protein_coding": true,
"protein_id": "NP_001018065.1",
"strand": true,
"transcript": "NM_001018055.3",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 291,
"aa_ref": "VQAV",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2769,
"cdna_start": 47,
"cds_end": null,
"cds_length": 876,
"cds_start": 27,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 11,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000330045.12",
"gene_hgnc_id": 24185,
"gene_symbol": "BRCC3",
"hgvs_c": "c.27_35delGCAGGCGGT",
"hgvs_p": "p.Gln10_Val12del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001018055.3",
"protein_coding": true,
"protein_id": "ENSP00000328641.7",
"strand": true,
"transcript": "ENST00000330045.12",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 316,
"aa_ref": "VQAV",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2846,
"cdna_start": 52,
"cds_end": null,
"cds_length": 951,
"cds_start": 27,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 12,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000369462.5",
"gene_hgnc_id": 24185,
"gene_symbol": "BRCC3",
"hgvs_c": "c.27_35delGCAGGCGGT",
"hgvs_p": "p.Gln10_Val12del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000358474.1",
"strand": true,
"transcript": "ENST00000369462.5",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 316,
"aa_ref": "VQAV",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2844,
"cdna_start": 47,
"cds_end": null,
"cds_length": 951,
"cds_start": 27,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 12,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_024332.4",
"gene_hgnc_id": 24185,
"gene_symbol": "BRCC3",
"hgvs_c": "c.27_35delGCAGGCGGT",
"hgvs_p": "p.Gln10_Val12del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_077308.1",
"strand": true,
"transcript": "NM_024332.4",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 292,
"aa_ref": "VQAV",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2772,
"cdna_start": 47,
"cds_end": null,
"cds_length": 879,
"cds_start": 27,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 11,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001242640.2",
"gene_hgnc_id": 24185,
"gene_symbol": "BRCC3",
"hgvs_c": "c.27_35delGCAGGCGGT",
"hgvs_p": "p.Gln10_Val12del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001229569.1",
"strand": true,
"transcript": "NM_001242640.2",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 292,
"aa_ref": "VQAV",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1101,
"cdna_start": 135,
"cds_end": null,
"cds_length": 879,
"cds_start": 27,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 11,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000340647.8",
"gene_hgnc_id": 24185,
"gene_symbol": "BRCC3",
"hgvs_c": "c.27_35delGCAGGCGGT",
"hgvs_p": "p.Gln10_Val12del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000344103.4",
"strand": true,
"transcript": "ENST00000340647.8",
"transcript_support_level": 2
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 247,
"aa_ref": "VQAV",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2641,
"cdna_start": 56,
"cds_end": null,
"cds_length": 744,
"cds_start": 27,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000369459.6",
"gene_hgnc_id": 24185,
"gene_symbol": "BRCC3",
"hgvs_c": "c.27_35delGCAGGCGGT",
"hgvs_p": "p.Gln10_Val12del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000358471.2",
"strand": true,
"transcript": "ENST00000369459.6",
"transcript_support_level": 5
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 225,
"aa_ref": "VQAV",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 688,
"cdna_start": 37,
"cds_end": null,
"cds_length": 678,
"cds_start": 27,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000411985.5",
"gene_hgnc_id": 24185,
"gene_symbol": "BRCC3",
"hgvs_c": "c.27_35delGCAGGCGGT",
"hgvs_p": "p.Gln10_Val12del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000413170.1",
"strand": true,
"transcript": "ENST00000411985.5",
"transcript_support_level": 5
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 317,
"aa_ref": "VQAV",
"aa_start": 9,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2847,
"cdna_start": 47,
"cds_end": null,
"cds_length": 954,
"cds_start": 27,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 12,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_005274751.5",
"gene_hgnc_id": 24185,
"gene_symbol": "BRCC3",
"hgvs_c": "c.27_35delGCAGGCGGT",
"hgvs_p": "p.Gln10_Val12del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005274808.1",
"strand": true,
"transcript": "XM_005274751.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 107,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 570,
"cdna_start": null,
"cds_end": null,
"cds_length": 324,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000362018.2",
"gene_hgnc_id": 7423,
"gene_symbol": "MTCP1",
"hgvs_c": "c.-47-5493_-47-5485delGCCTGCACC",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000355058.2",
"strand": false,
"transcript": "ENST00000362018.2",
"transcript_support_level": 3
},
{
"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": 2694,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000453705.1",
"gene_hgnc_id": 24185,
"gene_symbol": "BRCC3",
"hgvs_c": "n.21_29delGCAGGCGGT",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000415152.1",
"strand": true,
"transcript": "ENST00000453705.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 738,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000476116.1",
"gene_hgnc_id": 7423,
"gene_symbol": "MTCP1",
"hgvs_c": "n.279-5761_279-5753delGCCTGCACC",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000476116.1",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs782702164",
"effect": "disruptive_inframe_deletion",
"frequency_reference_population": 0.00058972155,
"gene_hgnc_id": 24185,
"gene_symbol": "BRCC3",
"gnomad_exomes_ac": 672,
"gnomad_exomes_af": 0.000615643,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 38,
"gnomad_genomes_af": 0.00033803,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 218,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.637,
"pos": 155071541,
"ref": "TGGTGCAGGC",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_024332.4"
}
]
}