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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: 15-38351124-CAT-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=38351124&ref=CAT&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 38351124,
"ref": "CAT",
"alt": "C",
"effect": "frameshift_variant",
"transcript": "NM_152594.3",
"consequences": [
{
"aa_ref": "M",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.796_797delAT",
"hgvs_p": "p.Met266fs",
"transcript": "NM_152594.3",
"protein_id": "NP_689807.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 444,
"cds_start": 796,
"cds_end": null,
"cds_length": 1335,
"cdna_start": 1146,
"cdna_end": null,
"cdna_length": 7270,
"mane_select": "ENST00000299084.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152594.3"
},
{
"aa_ref": "M",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.796_797delAT",
"hgvs_p": "p.Met266fs",
"transcript": "ENST00000299084.9",
"protein_id": "ENSP00000299084.4",
"transcript_support_level": 1,
"aa_start": 266,
"aa_end": null,
"aa_length": 444,
"cds_start": 796,
"cds_end": null,
"cds_length": 1335,
"cdna_start": 1146,
"cdna_end": null,
"cdna_length": 7270,
"mane_select": "NM_152594.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000299084.9"
},
{
"aa_ref": "M",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.832_833delAT",
"hgvs_p": "p.Met278fs",
"transcript": "ENST00000881380.1",
"protein_id": "ENSP00000551439.1",
"transcript_support_level": null,
"aa_start": 278,
"aa_end": null,
"aa_length": 456,
"cds_start": 832,
"cds_end": null,
"cds_length": 1371,
"cdna_start": 1274,
"cdna_end": null,
"cdna_length": 5083,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881380.1"
},
{
"aa_ref": "M",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.817_818delAT",
"hgvs_p": "p.Met273fs",
"transcript": "ENST00000951939.1",
"protein_id": "ENSP00000621998.1",
"transcript_support_level": null,
"aa_start": 273,
"aa_end": null,
"aa_length": 451,
"cds_start": 817,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1699,
"cdna_end": null,
"cdna_length": 4622,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951939.1"
},
{
"aa_ref": "M",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.796_797delAT",
"hgvs_p": "p.Met266fs",
"transcript": "ENST00000925370.1",
"protein_id": "ENSP00000595429.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 444,
"cds_start": 796,
"cds_end": null,
"cds_length": 1335,
"cdna_start": 849,
"cdna_end": null,
"cdna_length": 3776,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925370.1"
},
{
"aa_ref": "M",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.790_791delAT",
"hgvs_p": "p.Met264fs",
"transcript": "ENST00000881381.1",
"protein_id": "ENSP00000551440.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 442,
"cds_start": 790,
"cds_end": null,
"cds_length": 1329,
"cdna_start": 1701,
"cdna_end": null,
"cdna_length": 4608,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881381.1"
},
{
"aa_ref": "M",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.637_638delAT",
"hgvs_p": "p.Met213fs",
"transcript": "ENST00000951938.1",
"protein_id": "ENSP00000621997.1",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 391,
"cds_start": 637,
"cds_end": null,
"cds_length": 1176,
"cdna_start": 1622,
"cdna_end": null,
"cdna_length": 4546,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951938.1"
},
{
"aa_ref": "M",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.580_581delAT",
"hgvs_p": "p.Met194fs",
"transcript": "ENST00000951940.1",
"protein_id": "ENSP00000621999.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 372,
"cds_start": 580,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 1164,
"cdna_end": null,
"cdna_length": 4088,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951940.1"
},
{
"aa_ref": "M",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.421_422delAT",
"hgvs_p": "p.Met141fs",
"transcript": "ENST00000951937.1",
"protein_id": "ENSP00000621996.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 319,
"cds_start": 421,
"cds_end": null,
"cds_length": 960,
"cdna_start": 1468,
"cdna_end": null,
"cdna_length": 4392,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951937.1"
},
{
"aa_ref": "M",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.832_833delAT",
"hgvs_p": "p.Met278fs",
"transcript": "XM_005254202.4",
"protein_id": "XP_005254259.1",
"transcript_support_level": null,
"aa_start": 278,
"aa_end": null,
"aa_length": 456,
"cds_start": 832,
"cds_end": null,
"cds_length": 1371,
"cdna_start": 1182,
"cdna_end": null,
"cdna_length": 7306,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005254202.4"
},
{
"aa_ref": "M",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.733_734delAT",
"hgvs_p": "p.Met245fs",
"transcript": "XM_047432199.1",
"protein_id": "XP_047288155.1",
"transcript_support_level": null,
"aa_start": 245,
"aa_end": null,
"aa_length": 423,
"cds_start": 733,
"cds_end": null,
"cds_length": 1272,
"cdna_start": 1246,
"cdna_end": null,
"cdna_length": 7370,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047432199.1"
},
{
"aa_ref": "M",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.733_734delAT",
"hgvs_p": "p.Met245fs",
"transcript": "XM_047432200.1",
"protein_id": "XP_047288156.1",
"transcript_support_level": null,
"aa_start": 245,
"aa_end": null,
"aa_length": 423,
"cds_start": 733,
"cds_end": null,
"cds_length": 1272,
"cdna_start": 1210,
"cdna_end": null,
"cdna_length": 7334,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047432200.1"
},
{
"aa_ref": "M",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.733_734delAT",
"hgvs_p": "p.Met245fs",
"transcript": "XM_047432201.1",
"protein_id": "XP_047288157.1",
"transcript_support_level": null,
"aa_start": 245,
"aa_end": null,
"aa_length": 423,
"cds_start": 733,
"cds_end": null,
"cds_length": 1272,
"cdna_start": 883,
"cdna_end": null,
"cdna_length": 7007,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047432201.1"
}
],
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"dbsnp": "rs864622410",
"frequency_reference_population": 0.0000020522755,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205228,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"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": 6.215,
"phylop100way_prediction": "Uncertain_significance",
"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": 22,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PS3,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 22,
"benign_score": 0,
"pathogenic_score": 22,
"criteria": [
"PVS1",
"PS3",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_152594.3",
"gene_symbol": "SPRED1",
"hgnc_id": 20249,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.796_797delAT",
"hgvs_p": "p.Met266fs"
}
],
"clinvar_disease": "Cardiovascular phenotype,Legius syndrome,Noonan syndrome and Noonan-related syndrome,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:6 LP:1",
"phenotype_combined": "Legius syndrome|Noonan syndrome and Noonan-related syndrome|Cardiovascular phenotype|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}