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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: 19-38394767-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=38394767&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 38394767,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001042522.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "L",
"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": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.548G>T",
"hgvs_p": "p.Arg183Leu",
"transcript": "NM_001394336.1",
"protein_id": "NP_001381265.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 410,
"cds_start": 548,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000691638.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394336.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": true,
"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": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.548G>T",
"hgvs_p": "p.Arg183Leu",
"transcript": "ENST00000691638.1",
"protein_id": "ENSP00000510478.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 410,
"cds_start": 548,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001394336.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000691638.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"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": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.548G>T",
"hgvs_p": "p.Arg183Leu",
"transcript": "ENST00000338502.8",
"protein_id": "ENSP00000345405.4",
"transcript_support_level": 1,
"aa_start": 183,
"aa_end": null,
"aa_length": 410,
"cds_start": 548,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000338502.8"
},
{
"aa_ref": "R",
"aa_alt": "L",
"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": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.680G>T",
"hgvs_p": "p.Arg227Leu",
"transcript": "ENST00000587013.6",
"protein_id": "ENSP00000467540.1",
"transcript_support_level": 5,
"aa_start": 227,
"aa_end": null,
"aa_length": 454,
"cds_start": 680,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000587013.6"
},
{
"aa_ref": "R",
"aa_alt": "L",
"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": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.548G>T",
"hgvs_p": "p.Arg183Leu",
"transcript": "NM_001042522.3",
"protein_id": "NP_001035987.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 410,
"cds_start": 548,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001042522.3"
},
{
"aa_ref": "R",
"aa_alt": "L",
"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": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.548G>T",
"hgvs_p": "p.Arg183Leu",
"transcript": "ENST00000586301.6",
"protein_id": "ENSP00000466568.1",
"transcript_support_level": 5,
"aa_start": 183,
"aa_end": null,
"aa_length": 410,
"cds_start": 548,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000586301.6"
},
{
"aa_ref": "R",
"aa_alt": "L",
"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": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.548G>T",
"hgvs_p": "p.Arg183Leu",
"transcript": "ENST00000921746.1",
"protein_id": "ENSP00000591805.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 410,
"cds_start": 548,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921746.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"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": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.455G>T",
"hgvs_p": "p.Arg152Leu",
"transcript": "ENST00000921747.1",
"protein_id": "ENSP00000591806.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 379,
"cds_start": 455,
"cds_end": null,
"cds_length": 1140,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921747.1"
},
{
"aa_ref": "R",
"aa_alt": "L",
"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": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.44G>T",
"hgvs_p": "p.Arg15Leu",
"transcript": "NM_001394338.1",
"protein_id": "NP_001381267.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 242,
"cds_start": 44,
"cds_end": null,
"cds_length": 729,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394338.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.424-713G>T",
"hgvs_p": null,
"transcript": "NM_001394337.1",
"protein_id": "NP_001381266.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 362,
"cds_start": null,
"cds_end": null,
"cds_length": 1089,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394337.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "n.1083G>T",
"hgvs_p": null,
"transcript": "NR_073032.2",
"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_073032.2"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.*4G>T",
"hgvs_p": null,
"transcript": "ENST00000587947.5",
"protein_id": "ENSP00000467532.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 180,
"cds_start": null,
"cds_end": null,
"cds_length": 544,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000587947.5"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "n.*205G>T",
"hgvs_p": null,
"transcript": "ENST00000586958.1",
"protein_id": "ENSP00000465713.1",
"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": "ENST00000586958.1"
}
],
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"dbsnp": "rs865940339",
"frequency_reference_population": 0.000009139599,
"hom_count_reference_population": 0,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.0000091396,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1292610466480255,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.158,
"revel_prediction": "Benign",
"alphamissense_score": 0.1049,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.31,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.451,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_001042522.3",
"gene_symbol": "SPRED3",
"hgnc_id": 31041,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.548G>T",
"hgvs_p": "p.Arg183Leu"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}