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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: 1-8358216-TGGTGGA-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=8358216&ref=TGGTGGA&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 8358216,
"ref": "TGGTGGA",
"alt": "T",
"effect": "disruptive_inframe_deletion",
"transcript": "ENST00000400908.7",
"consequences": [
{
"aa_ref": "LHQ",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.4313_4318delTCCACC",
"hgvs_p": "p.Leu1438_His1439del",
"transcript": "NM_001042681.2",
"protein_id": "NP_001036146.1",
"transcript_support_level": null,
"aa_start": 1438,
"aa_end": null,
"aa_length": 1566,
"cds_start": 4313,
"cds_end": null,
"cds_length": 4701,
"cdna_start": 4943,
"cdna_end": null,
"cdna_length": 8009,
"mane_select": "ENST00000400908.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LHQ",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.4313_4318delTCCACC",
"hgvs_p": "p.Leu1438_His1439del",
"transcript": "ENST00000400908.7",
"protein_id": "ENSP00000383700.2",
"transcript_support_level": 1,
"aa_start": 1438,
"aa_end": null,
"aa_length": 1566,
"cds_start": 4313,
"cds_end": null,
"cds_length": 4701,
"cdna_start": 4943,
"cdna_end": null,
"cdna_length": 8009,
"mane_select": "NM_001042681.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LHQ",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.4313_4318delTCCACC",
"hgvs_p": "p.Leu1438_His1439del",
"transcript": "ENST00000337907.7",
"protein_id": "ENSP00000338629.3",
"transcript_support_level": 1,
"aa_start": 1438,
"aa_end": null,
"aa_length": 1566,
"cds_start": 4313,
"cds_end": null,
"cds_length": 4701,
"cdna_start": 4953,
"cdna_end": null,
"cdna_length": 8026,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LHQ",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.2651_2656delTCCACC",
"hgvs_p": "p.Leu884_His885del",
"transcript": "ENST00000476556.5",
"protein_id": "ENSP00000422246.1",
"transcript_support_level": 1,
"aa_start": 884,
"aa_end": null,
"aa_length": 1012,
"cds_start": 2651,
"cds_end": null,
"cds_length": 3039,
"cdna_start": 3221,
"cdna_end": null,
"cdna_length": 4598,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LHQ",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.4313_4318delTCCACC",
"hgvs_p": "p.Leu1438_His1439del",
"transcript": "NM_012102.4",
"protein_id": "NP_036234.3",
"transcript_support_level": null,
"aa_start": 1438,
"aa_end": null,
"aa_length": 1566,
"cds_start": 4313,
"cds_end": null,
"cds_length": 4701,
"cdna_start": 5128,
"cdna_end": null,
"cdna_length": 8194,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LHQ",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.3509_3514delTCCACC",
"hgvs_p": "p.Leu1170_His1171del",
"transcript": "ENST00000377464.5",
"protein_id": "ENSP00000366684.1",
"transcript_support_level": 5,
"aa_start": 1170,
"aa_end": null,
"aa_length": 1298,
"cds_start": 3509,
"cds_end": null,
"cds_length": 3897,
"cdna_start": 3669,
"cdna_end": null,
"cdna_length": 6733,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LHQ",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.2651_2656delTCCACC",
"hgvs_p": "p.Leu884_His885del",
"transcript": "NM_001042682.2",
"protein_id": "NP_001036147.1",
"transcript_support_level": null,
"aa_start": 884,
"aa_end": null,
"aa_length": 1012,
"cds_start": 2651,
"cds_end": null,
"cds_length": 3039,
"cdna_start": 3387,
"cdna_end": null,
"cdna_length": 6453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LHQ",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.2651_2656delTCCACC",
"hgvs_p": "p.Leu884_His885del",
"transcript": "ENST00000465125.2",
"protein_id": "ENSP00000515651.1",
"transcript_support_level": 5,
"aa_start": 884,
"aa_end": null,
"aa_length": 1012,
"cds_start": 2651,
"cds_end": null,
"cds_length": 3039,
"cdna_start": 3335,
"cdna_end": null,
"cdna_length": 6395,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.1541-2623_1541-2618delTCCACC",
"hgvs_p": null,
"transcript": "ENST00000400907.6",
"protein_id": "ENSP00000383699.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 584,
"cds_start": -4,
"cds_end": null,
"cds_length": 1755,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2973,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"hgvs_c": "c.308-1976_308-1971delTCCACC",
"hgvs_p": null,
"transcript": "ENST00000505225.1",
"protein_id": "ENSP00000423451.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 176,
"cds_start": -4,
"cds_end": null,
"cds_length": 533,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 533,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RERE",
"gene_hgnc_id": 9965,
"dbsnp": "rs1064793252",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 9.974,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PP3,PP5_Very_Strong,BP3",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 1,
"pathogenic_score": 13,
"criteria": [
"PM1",
"PM2",
"PP3",
"PP5_Very_Strong",
"BP3"
],
"verdict": "Pathogenic",
"transcript": "ENST00000400908.7",
"gene_symbol": "RERE",
"hgnc_id": 9965,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "AD",
"hgvs_c": "c.4313_4318delTCCACC",
"hgvs_p": "p.Leu1438_His1439del"
}
],
"clinvar_disease": " eye, or heart,Neurodevelopmental disorder with or without anomalies of the brain,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3",
"phenotype_combined": "not provided|Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}