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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: 5-1053281-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=1053281&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "SLC12A7",
"hgnc_id": 10915,
"hgvs_c": "c.3160+68G>T",
"hgvs_p": null,
"inheritance_mode": "Unknown",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_006598.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 6,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.88,
"chr": "5",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8799999952316284,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1083,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5300,
"cdna_start": null,
"cds_end": null,
"cds_length": 3252,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 24,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_006598.3",
"gene_hgnc_id": 10915,
"gene_symbol": "SLC12A7",
"hgvs_c": "c.3160+68G>T",
"hgvs_p": null,
"intron_rank": 23,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000264930.10",
"protein_coding": true,
"protein_id": "NP_006589.2",
"strand": false,
"transcript": "NM_006598.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1083,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5300,
"cdna_start": null,
"cds_end": null,
"cds_length": 3252,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 24,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000264930.10",
"gene_hgnc_id": 10915,
"gene_symbol": "SLC12A7",
"hgvs_c": "c.3160+68G>T",
"hgvs_p": null,
"intron_rank": 23,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006598.3",
"protein_coding": true,
"protein_id": "ENSP00000264930.5",
"strand": false,
"transcript": "ENST00000264930.10",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 988,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3142,
"cdna_start": null,
"cds_end": null,
"cds_length": 2967,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 23,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000634447.1",
"gene_hgnc_id": 10915,
"gene_symbol": "SLC12A7",
"hgvs_c": "c.2875+68G>T",
"hgvs_p": null,
"intron_rank": 22,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000489285.1",
"strand": false,
"transcript": "ENST00000634447.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1122,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5343,
"cdna_start": null,
"cds_end": null,
"cds_length": 3369,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000945163.1",
"gene_hgnc_id": 10915,
"gene_symbol": "SLC12A7",
"hgvs_c": "c.3277+68G>T",
"hgvs_p": null,
"intron_rank": 25,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000615222.1",
"strand": false,
"transcript": "ENST00000945163.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1106,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5347,
"cdna_start": null,
"cds_end": null,
"cds_length": 3321,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 24,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000851006.1",
"gene_hgnc_id": 10915,
"gene_symbol": "SLC12A7",
"hgvs_c": "c.3229+68G>T",
"hgvs_p": null,
"intron_rank": 23,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000521081.1",
"strand": false,
"transcript": "ENST00000851006.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1088,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5319,
"cdna_start": null,
"cds_end": null,
"cds_length": 3267,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 24,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000922388.1",
"gene_hgnc_id": 10915,
"gene_symbol": "SLC12A7",
"hgvs_c": "c.3175+68G>T",
"hgvs_p": null,
"intron_rank": 23,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592447.1",
"strand": false,
"transcript": "ENST00000922388.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 495,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3505,
"cdna_start": null,
"cds_end": null,
"cds_length": 1488,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000902220.1",
"gene_hgnc_id": 10915,
"gene_symbol": "SLC12A7",
"hgvs_c": "c.1397-830G>T",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000572279.1",
"strand": false,
"transcript": "ENST00000902220.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1111,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5345,
"cdna_start": null,
"cds_end": null,
"cds_length": 3336,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 25,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011513941.3",
"gene_hgnc_id": 10915,
"gene_symbol": "SLC12A7",
"hgvs_c": "c.3244+68G>T",
"hgvs_p": null,
"intron_rank": 24,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512243.2",
"strand": false,
"transcript": "XM_011513941.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1088,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5315,
"cdna_start": null,
"cds_end": null,
"cds_length": 3267,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 25,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_005248231.4",
"gene_hgnc_id": 10915,
"gene_symbol": "SLC12A7",
"hgvs_c": "c.3175+68G>T",
"hgvs_p": null,
"intron_rank": 24,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005248288.1",
"strand": false,
"transcript": "XM_005248231.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1085,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5306,
"cdna_start": null,
"cds_end": null,
"cds_length": 3258,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 25,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011513939.4",
"gene_hgnc_id": 10915,
"gene_symbol": "SLC12A7",
"hgvs_c": "c.3166+68G>T",
"hgvs_p": null,
"intron_rank": 24,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512241.1",
"strand": false,
"transcript": "XM_011513939.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1074,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5998,
"cdna_start": null,
"cds_end": null,
"cds_length": 3225,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 25,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011513940.3",
"gene_hgnc_id": 10915,
"gene_symbol": "SLC12A7",
"hgvs_c": "c.3133+68G>T",
"hgvs_p": null,
"intron_rank": 24,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512242.1",
"strand": false,
"transcript": "XM_011513940.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1020,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5611,
"cdna_start": null,
"cds_end": null,
"cds_length": 3063,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 25,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017008958.2",
"gene_hgnc_id": 10915,
"gene_symbol": "SLC12A7",
"hgvs_c": "c.2971+68G>T",
"hgvs_p": null,
"intron_rank": 24,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864447.1",
"strand": false,
"transcript": "XM_017008958.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1020,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5201,
"cdna_start": null,
"cds_end": null,
"cds_length": 3063,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 25,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047416640.1",
"gene_hgnc_id": 10915,
"gene_symbol": "SLC12A7",
"hgvs_c": "c.2971+68G>T",
"hgvs_p": null,
"intron_rank": 24,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047272596.1",
"strand": false,
"transcript": "XM_047416640.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs2241603",
"effect": "intron_variant",
"frequency_reference_population": 0.0000042698125,
"gene_hgnc_id": 10915,
"gene_symbol": "SLC12A7",
"gnomad_exomes_ac": 6,
"gnomad_exomes_af": 0.00000426981,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.649,
"pos": 1053281,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_006598.3"
}
]
}