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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: 2-197401887-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=197401887&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 197401887,
"ref": "C",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_012433.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "c.2225G>T",
"hgvs_p": "p.Gly742Val",
"transcript": "NM_012433.4",
"protein_id": "NP_036565.2",
"transcript_support_level": null,
"aa_start": 742,
"aa_end": null,
"aa_length": 1304,
"cds_start": 2225,
"cds_end": null,
"cds_length": 3915,
"cdna_start": 2254,
"cdna_end": null,
"cdna_length": 6463,
"mane_select": "ENST00000335508.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "c.2225G>T",
"hgvs_p": "p.Gly742Val",
"transcript": "ENST00000335508.11",
"protein_id": "ENSP00000335321.6",
"transcript_support_level": 1,
"aa_start": 742,
"aa_end": null,
"aa_length": 1304,
"cds_start": 2225,
"cds_end": null,
"cds_length": 3915,
"cdna_start": 2254,
"cdna_end": null,
"cdna_length": 6463,
"mane_select": "NM_012433.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "c.1787G>T",
"hgvs_p": "p.Gly596Val",
"transcript": "XM_047443838.1",
"protein_id": "XP_047299794.1",
"transcript_support_level": null,
"aa_start": 596,
"aa_end": null,
"aa_length": 1158,
"cds_start": 1787,
"cds_end": null,
"cds_length": 3477,
"cdna_start": 3519,
"cdna_end": null,
"cdna_length": 7728,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "c.1787G>T",
"hgvs_p": "p.Gly596Val",
"transcript": "XM_047443839.1",
"protein_id": "XP_047299795.1",
"transcript_support_level": null,
"aa_start": 596,
"aa_end": null,
"aa_length": 1158,
"cds_start": 1787,
"cds_end": null,
"cds_length": 3477,
"cdna_start": 3235,
"cdna_end": null,
"cdna_length": 7444,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "c.2225G>T",
"hgvs_p": "p.Gly742Val",
"transcript": "XM_047443840.1",
"protein_id": "XP_047299796.1",
"transcript_support_level": null,
"aa_start": 742,
"aa_end": null,
"aa_length": 1030,
"cds_start": 2225,
"cds_end": null,
"cds_length": 3093,
"cdna_start": 2319,
"cdna_end": null,
"cdna_length": 3248,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "n.4109G>T",
"hgvs_p": null,
"transcript": "ENST00000470268.2",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8308,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "n.*3292G>T",
"hgvs_p": null,
"transcript": "ENST00000652026.1",
"protein_id": "ENSP00000498652.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9283,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "n.*2484G>T",
"hgvs_p": null,
"transcript": "ENST00000652738.1",
"protein_id": "ENSP00000499119.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8478,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "n.*3292G>T",
"hgvs_p": null,
"transcript": "ENST00000652026.1",
"protein_id": "ENSP00000498652.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9283,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "n.*2484G>T",
"hgvs_p": null,
"transcript": "ENST00000652738.1",
"protein_id": "ENSP00000499119.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8478,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"hgvs_c": "n.*135G>T",
"hgvs_p": null,
"transcript": "ENST00000462613.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 141,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SF3B1",
"gene_hgnc_id": 10768,
"dbsnp": "rs755415626",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6458324790000916,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.09600000083446503,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.388,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7805,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.11,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.847,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.03,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000123432323746938,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_012433.4",
"gene_symbol": "SF3B1",
"hgnc_id": 10768,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2225G>T",
"hgvs_p": "p.Gly742Val"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}