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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: 15-38349426-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=38349426&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 38349426,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_152594.3",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.587C>T",
"hgvs_p": "p.Thr196Ile",
"transcript": "NM_152594.3",
"protein_id": "NP_689807.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 444,
"cds_start": 587,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000299084.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152594.3"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.587C>T",
"hgvs_p": "p.Thr196Ile",
"transcript": "ENST00000299084.9",
"protein_id": "ENSP00000299084.4",
"transcript_support_level": 1,
"aa_start": 196,
"aa_end": null,
"aa_length": 444,
"cds_start": 587,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_152594.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000299084.9"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.623C>T",
"hgvs_p": "p.Thr208Ile",
"transcript": "ENST00000881380.1",
"protein_id": "ENSP00000551439.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 456,
"cds_start": 623,
"cds_end": null,
"cds_length": 1371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881380.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.608C>T",
"hgvs_p": "p.Thr203Ile",
"transcript": "ENST00000951939.1",
"protein_id": "ENSP00000621998.1",
"transcript_support_level": null,
"aa_start": 203,
"aa_end": null,
"aa_length": 451,
"cds_start": 608,
"cds_end": null,
"cds_length": 1356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951939.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.587C>T",
"hgvs_p": "p.Thr196Ile",
"transcript": "ENST00000925370.1",
"protein_id": "ENSP00000595429.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 444,
"cds_start": 587,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925370.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.581C>T",
"hgvs_p": "p.Thr194Ile",
"transcript": "ENST00000881381.1",
"protein_id": "ENSP00000551440.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 442,
"cds_start": 581,
"cds_end": null,
"cds_length": 1329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881381.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.428C>T",
"hgvs_p": "p.Thr143Ile",
"transcript": "ENST00000951938.1",
"protein_id": "ENSP00000621997.1",
"transcript_support_level": null,
"aa_start": 143,
"aa_end": null,
"aa_length": 391,
"cds_start": 428,
"cds_end": null,
"cds_length": 1176,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951938.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.371C>T",
"hgvs_p": "p.Thr124Ile",
"transcript": "ENST00000951940.1",
"protein_id": "ENSP00000621999.1",
"transcript_support_level": null,
"aa_start": 124,
"aa_end": null,
"aa_length": 372,
"cds_start": 371,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951940.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.212C>T",
"hgvs_p": "p.Thr71Ile",
"transcript": "ENST00000951937.1",
"protein_id": "ENSP00000621996.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 319,
"cds_start": 212,
"cds_end": null,
"cds_length": 960,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951937.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.623C>T",
"hgvs_p": "p.Thr208Ile",
"transcript": "XM_005254202.4",
"protein_id": "XP_005254259.1",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 456,
"cds_start": 623,
"cds_end": null,
"cds_length": 1371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005254202.4"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.524C>T",
"hgvs_p": "p.Thr175Ile",
"transcript": "XM_047432199.1",
"protein_id": "XP_047288155.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 423,
"cds_start": 524,
"cds_end": null,
"cds_length": 1272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047432199.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.524C>T",
"hgvs_p": "p.Thr175Ile",
"transcript": "XM_047432200.1",
"protein_id": "XP_047288156.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 423,
"cds_start": 524,
"cds_end": null,
"cds_length": 1272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047432200.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"hgvs_c": "c.524C>T",
"hgvs_p": "p.Thr175Ile",
"transcript": "XM_047432201.1",
"protein_id": "XP_047288157.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 423,
"cds_start": 524,
"cds_end": null,
"cds_length": 1272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047432201.1"
}
],
"gene_symbol": "SPRED1",
"gene_hgnc_id": 20249,
"dbsnp": "rs147474792",
"frequency_reference_population": 0.00010317275,
"hom_count_reference_population": 1,
"allele_count_reference_population": 166,
"gnomad_exomes_af": 0.000106395,
"gnomad_genomes_af": 0.0000723161,
"gnomad_exomes_ac": 155,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.061833590269088745,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.128,
"revel_prediction": "Benign",
"alphamissense_score": 0.0809,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.493,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_152594.3",
"gene_symbol": "SPRED1",
"hgnc_id": 20249,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.587C>T",
"hgvs_p": "p.Thr196Ile"
}
],
"clinvar_disease": "Cardiovascular phenotype,Legius syndrome,Noonan syndrome and Noonan-related syndrome,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:5 LB:3 B:2",
"phenotype_combined": "not specified|Legius syndrome|Noonan syndrome and Noonan-related syndrome|not provided|Cardiovascular phenotype",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}