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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-23783385-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=23783385&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 23783385,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_002970.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAT1",
"gene_hgnc_id": 10540,
"hgvs_c": "c.34G>A",
"hgvs_p": "p.Ala12Thr",
"transcript": "NM_002970.4",
"protein_id": "NP_002961.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 171,
"cds_start": 34,
"cds_end": null,
"cds_length": 516,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000379270.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002970.4"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAT1",
"gene_hgnc_id": 10540,
"hgvs_c": "c.34G>A",
"hgvs_p": "p.Ala12Thr",
"transcript": "ENST00000379270.5",
"protein_id": "ENSP00000368572.4",
"transcript_support_level": 1,
"aa_start": 12,
"aa_end": null,
"aa_length": 171,
"cds_start": 34,
"cds_end": null,
"cds_length": 516,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002970.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379270.5"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAT1",
"gene_hgnc_id": 10540,
"hgvs_c": "c.34G>A",
"hgvs_p": "p.Ala12Thr",
"transcript": "ENST00000379254.5",
"protein_id": "ENSP00000368556.1",
"transcript_support_level": 3,
"aa_start": 12,
"aa_end": null,
"aa_length": 143,
"cds_start": 34,
"cds_end": null,
"cds_length": 432,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379254.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAT1",
"gene_hgnc_id": 10540,
"hgvs_c": "n.213G>A",
"hgvs_p": null,
"transcript": "ENST00000379251.7",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000379251.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAT1",
"gene_hgnc_id": 10540,
"hgvs_c": "n.213G>A",
"hgvs_p": null,
"transcript": "ENST00000379253.7",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000379253.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAT1",
"gene_hgnc_id": 10540,
"hgvs_c": "n.34G>A",
"hgvs_p": null,
"transcript": "ENST00000489394.5",
"protein_id": "ENSP00000506998.1",
"transcript_support_level": 2,
"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": "nonsense_mediated_decay",
"feature": "ENST00000489394.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAT1-DT",
"gene_hgnc_id": 56726,
"hgvs_c": "n.22C>T",
"hgvs_p": null,
"transcript": "ENST00000737050.1",
"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": "ENST00000737050.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAT1",
"gene_hgnc_id": 10540,
"hgvs_c": "n.213G>A",
"hgvs_p": null,
"transcript": "NR_027783.3",
"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_027783.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC127933115",
"gene_hgnc_id": 0,
"hgvs_c": "c.*18G>A",
"hgvs_p": null,
"transcript": "NM_001414725.1",
"protein_id": "NP_001401654.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 29,
"cds_start": null,
"cds_end": null,
"cds_length": 90,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000683890.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001414725.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288706",
"gene_hgnc_id": 0,
"hgvs_c": "c.*18G>A",
"hgvs_p": null,
"transcript": "ENST00000683890.1",
"protein_id": "ENSP00000506989.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 29,
"cds_start": null,
"cds_end": null,
"cds_length": 90,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001414725.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000683890.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SAT1",
"gene_hgnc_id": 10540,
"hgvs_c": "n.-123G>A",
"hgvs_p": null,
"transcript": "ENST00000487713.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000487713.1"
}
],
"gene_symbol": "SAT1",
"gene_hgnc_id": 10540,
"dbsnp": "rs145980431",
"frequency_reference_population": 0.00045894168,
"hom_count_reference_population": 159,
"allele_count_reference_population": 555,
"gnomad_exomes_af": 0.000480369,
"gnomad_genomes_af": 0.000249488,
"gnomad_exomes_ac": 527,
"gnomad_genomes_ac": 28,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05160781741142273,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.036,
"revel_prediction": "Benign",
"alphamissense_score": 0.0916,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.72,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.858,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_002970.4",
"gene_symbol": "SAT1",
"hgnc_id": 10540,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.34G>A",
"hgvs_p": "p.Ala12Thr"
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000737050.1",
"gene_symbol": "SAT1-DT",
"hgnc_id": 56726,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.22C>T",
"hgvs_p": null
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001414725.1",
"gene_symbol": "LOC127933115",
"hgnc_id": 0,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*18G>A",
"hgvs_p": null
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000683890.1",
"gene_symbol": "ENSG00000288706",
"hgnc_id": 0,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*18G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}