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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-148980756-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=148980756&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 148980756,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_002025.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF2",
"gene_hgnc_id": 3776,
"hgvs_c": "c.3589G>A",
"hgvs_p": "p.Ala1197Thr",
"transcript": "NM_002025.4",
"protein_id": "NP_002016.2",
"transcript_support_level": null,
"aa_start": 1197,
"aa_end": null,
"aa_length": 1311,
"cds_start": 3589,
"cds_end": null,
"cds_length": 3936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000370460.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002025.4"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF2",
"gene_hgnc_id": 3776,
"hgvs_c": "c.3589G>A",
"hgvs_p": "p.Ala1197Thr",
"transcript": "ENST00000370460.7",
"protein_id": "ENSP00000359489.2",
"transcript_support_level": 5,
"aa_start": 1197,
"aa_end": null,
"aa_length": 1311,
"cds_start": 3589,
"cds_end": null,
"cds_length": 3936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002025.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370460.7"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF2",
"gene_hgnc_id": 3776,
"hgvs_c": "c.3484G>A",
"hgvs_p": "p.Ala1162Thr",
"transcript": "ENST00000342251.7",
"protein_id": "ENSP00000345459.4",
"transcript_support_level": 1,
"aa_start": 1162,
"aa_end": null,
"aa_length": 1276,
"cds_start": 3484,
"cds_end": null,
"cds_length": 3831,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000342251.7"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF2",
"gene_hgnc_id": 3776,
"hgvs_c": "c.3484G>A",
"hgvs_p": "p.Ala1162Thr",
"transcript": "ENST00000370457.9",
"protein_id": "ENSP00000359486.6",
"transcript_support_level": 1,
"aa_start": 1162,
"aa_end": null,
"aa_length": 1276,
"cds_start": 3484,
"cds_end": null,
"cds_length": 3831,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370457.9"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF2",
"gene_hgnc_id": 3776,
"hgvs_c": "c.3559G>A",
"hgvs_p": "p.Ala1187Thr",
"transcript": "NM_001169123.2",
"protein_id": "NP_001162594.1",
"transcript_support_level": null,
"aa_start": 1187,
"aa_end": null,
"aa_length": 1301,
"cds_start": 3559,
"cds_end": null,
"cds_length": 3906,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001169123.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF2",
"gene_hgnc_id": 3776,
"hgvs_c": "c.3484G>A",
"hgvs_p": "p.Ala1162Thr",
"transcript": "NM_001169122.2",
"protein_id": "NP_001162593.1",
"transcript_support_level": null,
"aa_start": 1162,
"aa_end": null,
"aa_length": 1276,
"cds_start": 3484,
"cds_end": null,
"cds_length": 3831,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001169122.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF2",
"gene_hgnc_id": 3776,
"hgvs_c": "c.3484G>A",
"hgvs_p": "p.Ala1162Thr",
"transcript": "NM_001169124.2",
"protein_id": "NP_001162595.1",
"transcript_support_level": null,
"aa_start": 1162,
"aa_end": null,
"aa_length": 1276,
"cds_start": 3484,
"cds_end": null,
"cds_length": 3831,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001169124.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF2",
"gene_hgnc_id": 3776,
"hgvs_c": "c.3472G>A",
"hgvs_p": "p.Ala1158Thr",
"transcript": "NM_001169125.2",
"protein_id": "NP_001162596.1",
"transcript_support_level": null,
"aa_start": 1158,
"aa_end": null,
"aa_length": 1272,
"cds_start": 3472,
"cds_end": null,
"cds_length": 3819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001169125.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF2",
"gene_hgnc_id": 3776,
"hgvs_c": "c.2512G>A",
"hgvs_p": "p.Ala838Thr",
"transcript": "NM_001170628.1",
"protein_id": "NP_001164099.1",
"transcript_support_level": null,
"aa_start": 838,
"aa_end": null,
"aa_length": 952,
"cds_start": 2512,
"cds_end": null,
"cds_length": 2859,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001170628.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF2",
"gene_hgnc_id": 3776,
"hgvs_c": "c.2512G>A",
"hgvs_p": "p.Ala838Thr",
"transcript": "ENST00000286437.7",
"protein_id": "ENSP00000286437.5",
"transcript_support_level": 2,
"aa_start": 838,
"aa_end": null,
"aa_length": 952,
"cds_start": 2512,
"cds_end": null,
"cds_length": 2859,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000286437.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF2",
"gene_hgnc_id": 3776,
"hgvs_c": "n.2602G>A",
"hgvs_p": null,
"transcript": "ENST00000671877.1",
"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": "ENST00000671877.1"
}
],
"gene_symbol": "AFF2",
"gene_hgnc_id": 3776,
"dbsnp": "rs373659849",
"frequency_reference_population": 0.0000267784,
"hom_count_reference_population": 16,
"allele_count_reference_population": 32,
"gnomad_exomes_af": 0.0000175367,
"gnomad_genomes_af": 0.00011654,
"gnomad_exomes_ac": 19,
"gnomad_genomes_ac": 13,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03298920392990112,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.162,
"revel_prediction": "Benign",
"alphamissense_score": 0.0666,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.72,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.471,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS1_Supporting",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_002025.4",
"gene_symbol": "AFF2",
"hgnc_id": 3776,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.3589G>A",
"hgvs_p": "p.Ala1197Thr"
}
],
"clinvar_disease": "Inborn genetic diseases,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not specified|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}