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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: 14-21522069-AG-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=21522069&ref=AG&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 21522069,
"ref": "AG",
"alt": "A",
"effect": "frameshift_variant",
"transcript": "NM_001291446.2",
"consequences": [
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL2",
"gene_hgnc_id": 10526,
"hgvs_c": "c.560delC",
"hgvs_p": "p.Pro187fs",
"transcript": "ENST00000611430.4",
"protein_id": "ENSP00000484460.1",
"transcript_support_level": 1,
"aa_start": 187,
"aa_end": null,
"aa_length": 198,
"cds_start": 560,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000611430.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL2",
"gene_hgnc_id": 10526,
"hgvs_c": "c.*634delC",
"hgvs_p": null,
"transcript": "NM_001364564.1",
"protein_id": "NP_001351493.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1005,
"cds_start": null,
"cds_end": null,
"cds_length": 3018,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000537235.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001364564.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL2",
"gene_hgnc_id": 10526,
"hgvs_c": "c.*634delC",
"hgvs_p": null,
"transcript": "ENST00000537235.2",
"protein_id": "ENSP00000438493.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 1005,
"cds_start": null,
"cds_end": null,
"cds_length": 3018,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001364564.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000537235.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL2",
"gene_hgnc_id": 10526,
"hgvs_c": "c.*634delC",
"hgvs_p": null,
"transcript": "ENST00000614342.1",
"protein_id": "ENSP00000483562.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1007,
"cds_start": null,
"cds_end": null,
"cds_length": 3024,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000614342.1"
},
{
"aa_ref": "L",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL2",
"gene_hgnc_id": 10526,
"hgvs_c": "c.2665delC",
"hgvs_p": "p.Leu889fs",
"transcript": "NM_001291446.2",
"protein_id": "NP_001278375.1",
"transcript_support_level": null,
"aa_start": 889,
"aa_end": null,
"aa_length": 908,
"cds_start": 2665,
"cds_end": null,
"cds_length": 2727,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001291446.2"
},
{
"aa_ref": "L",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL2",
"gene_hgnc_id": 10526,
"hgvs_c": "c.2659delC",
"hgvs_p": "p.Leu887fs",
"transcript": "NM_001291447.2",
"protein_id": "NP_001278376.1",
"transcript_support_level": null,
"aa_start": 887,
"aa_end": null,
"aa_length": 906,
"cds_start": 2659,
"cds_end": null,
"cds_length": 2721,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001291447.2"
},
{
"aa_ref": "L",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL2",
"gene_hgnc_id": 10526,
"hgvs_c": "c.2659delC",
"hgvs_p": "p.Leu887fs",
"transcript": "ENST00000450879.2",
"protein_id": "ENSP00000396773.2",
"transcript_support_level": 2,
"aa_start": 887,
"aa_end": null,
"aa_length": 906,
"cds_start": 2659,
"cds_end": null,
"cds_length": 2721,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000450879.2"
},
{
"aa_ref": "L",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL2",
"gene_hgnc_id": 10526,
"hgvs_c": "c.2644delC",
"hgvs_p": "p.Leu882fs",
"transcript": "ENST00000546363.5",
"protein_id": "ENSP00000440054.1",
"transcript_support_level": 2,
"aa_start": 882,
"aa_end": null,
"aa_length": 901,
"cds_start": 2644,
"cds_end": null,
"cds_length": 2706,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000546363.5"
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL2",
"gene_hgnc_id": 10526,
"hgvs_c": "c.566delC",
"hgvs_p": "p.Pro189fs",
"transcript": "ENST00000613414.4",
"protein_id": "ENSP00000483202.1",
"transcript_support_level": 2,
"aa_start": 189,
"aa_end": null,
"aa_length": 200,
"cds_start": 566,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000613414.4"
},
{
"aa_ref": "L",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL2",
"gene_hgnc_id": 10526,
"hgvs_c": "c.3070delC",
"hgvs_p": "p.Leu1024fs",
"transcript": "XM_011537064.2",
"protein_id": "XP_011535366.1",
"transcript_support_level": null,
"aa_start": 1024,
"aa_end": null,
"aa_length": 1043,
"cds_start": 3070,
"cds_end": null,
"cds_length": 3132,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011537064.2"
},
{
"aa_ref": "L",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL2",
"gene_hgnc_id": 10526,
"hgvs_c": "c.3064delC",
"hgvs_p": "p.Leu1022fs",
"transcript": "XM_011537065.3",
"protein_id": "XP_011535367.1",
"transcript_support_level": null,
"aa_start": 1022,
"aa_end": null,
"aa_length": 1041,
"cds_start": 3064,
"cds_end": null,
"cds_length": 3126,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011537065.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL2",
"gene_hgnc_id": 10526,
"hgvs_c": "c.*634delC",
"hgvs_p": null,
"transcript": "NM_005407.3",
"protein_id": "NP_005398.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1007,
"cds_start": null,
"cds_end": null,
"cds_length": 3024,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005407.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL2",
"gene_hgnc_id": 10526,
"hgvs_c": "n.766delC",
"hgvs_p": null,
"transcript": "NR_111966.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_111966.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SALL2",
"gene_hgnc_id": 10526,
"hgvs_c": "n.779delC",
"hgvs_p": null,
"transcript": "NR_111967.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_111967.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000257096",
"gene_hgnc_id": null,
"hgvs_c": "n.218-331delG",
"hgvs_p": null,
"transcript": "ENST00000535893.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000535893.1"
}
],
"gene_symbol": "SALL2",
"gene_hgnc_id": 10526,
"dbsnp": "rs576985829",
"frequency_reference_population": 0.00063915725,
"hom_count_reference_population": 2,
"allele_count_reference_population": 1021,
"gnomad_exomes_af": 0.000613713,
"gnomad_genomes_af": 0.000880907,
"gnomad_exomes_ac": 887,
"gnomad_genomes_ac": 134,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.509,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_001291446.2",
"gene_symbol": "SALL2",
"hgnc_id": 10526,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.2665delC",
"hgvs_p": "p.Leu889fs"
},
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000535893.1",
"gene_symbol": "ENSG00000257096",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.218-331delG",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive, ocular,Coloboma",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Coloboma, ocular, autosomal recessive",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}