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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: 19-38390478-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=38390478&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 38390478,
"ref": "A",
"alt": "G",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_001042522.3",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.176A>G",
"hgvs_p": "p.Lys59Arg",
"transcript": "NM_001394336.1",
"protein_id": "NP_001381265.1",
"transcript_support_level": null,
"aa_start": 59,
"aa_end": null,
"aa_length": 410,
"cds_start": 176,
"cds_end": null,
"cds_length": 1233,
"cdna_start": 291,
"cdna_end": null,
"cdna_length": 4790,
"mane_select": "ENST00000691638.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394336.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.176A>G",
"hgvs_p": "p.Lys59Arg",
"transcript": "ENST00000691638.1",
"protein_id": "ENSP00000510478.1",
"transcript_support_level": null,
"aa_start": 59,
"aa_end": null,
"aa_length": 410,
"cds_start": 176,
"cds_end": null,
"cds_length": 1233,
"cdna_start": 291,
"cdna_end": null,
"cdna_length": 4790,
"mane_select": "NM_001394336.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000691638.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.176A>G",
"hgvs_p": "p.Lys59Arg",
"transcript": "ENST00000338502.8",
"protein_id": "ENSP00000345405.4",
"transcript_support_level": 1,
"aa_start": 59,
"aa_end": null,
"aa_length": 410,
"cds_start": 176,
"cds_end": null,
"cds_length": 1233,
"cdna_start": 279,
"cdna_end": null,
"cdna_length": 4778,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000338502.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "n.180A>G",
"hgvs_p": null,
"transcript": "ENST00000587564.2",
"protein_id": null,
"transcript_support_level": 1,
"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": 543,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000587564.2"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.176A>G",
"hgvs_p": "p.Lys59Arg",
"transcript": "NM_001042522.3",
"protein_id": "NP_001035987.1",
"transcript_support_level": null,
"aa_start": 59,
"aa_end": null,
"aa_length": 410,
"cds_start": 176,
"cds_end": null,
"cds_length": 1233,
"cdna_start": 688,
"cdna_end": null,
"cdna_length": 5187,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001042522.3"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.176A>G",
"hgvs_p": "p.Lys59Arg",
"transcript": "ENST00000586301.6",
"protein_id": "ENSP00000466568.1",
"transcript_support_level": 5,
"aa_start": 59,
"aa_end": null,
"aa_length": 410,
"cds_start": 176,
"cds_end": null,
"cds_length": 1233,
"cdna_start": 306,
"cdna_end": null,
"cdna_length": 4805,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000586301.6"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.176A>G",
"hgvs_p": "p.Lys59Arg",
"transcript": "ENST00000921746.1",
"protein_id": "ENSP00000591805.1",
"transcript_support_level": null,
"aa_start": 59,
"aa_end": null,
"aa_length": 410,
"cds_start": 176,
"cds_end": null,
"cds_length": 1233,
"cdna_start": 294,
"cdna_end": null,
"cdna_length": 4794,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921746.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.176A>G",
"hgvs_p": "p.Lys59Arg",
"transcript": "NM_001394337.1",
"protein_id": "NP_001381266.1",
"transcript_support_level": null,
"aa_start": 59,
"aa_end": null,
"aa_length": 362,
"cds_start": 176,
"cds_end": null,
"cds_length": 1089,
"cdna_start": 291,
"cdna_end": null,
"cdna_length": 4646,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394337.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.176A>G",
"hgvs_p": "p.Lys59Arg",
"transcript": "ENST00000587947.5",
"protein_id": "ENSP00000467532.1",
"transcript_support_level": 3,
"aa_start": 59,
"aa_end": null,
"aa_length": 180,
"cds_start": 176,
"cds_end": null,
"cds_length": 544,
"cdna_start": 278,
"cdna_end": null,
"cdna_length": 646,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000587947.5"
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.310-1468A>G",
"hgvs_p": null,
"transcript": "ENST00000587013.6",
"protein_id": "ENSP00000467540.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 454,
"cds_start": null,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4885,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000587013.6"
},
{
"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": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.84+92A>G",
"hgvs_p": null,
"transcript": "ENST00000921747.1",
"protein_id": "ENSP00000591806.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 379,
"cds_start": null,
"cds_end": null,
"cds_length": 1140,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4696,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921747.1"
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "c.-327-1468A>G",
"hgvs_p": null,
"transcript": "NM_001394338.1",
"protein_id": "NP_001381267.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 242,
"cds_start": null,
"cds_end": null,
"cds_length": 729,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4609,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394338.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "n.84+92A>G",
"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": 478,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000586958.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"hgvs_c": "n.596+92A>G",
"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": 5210,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_073032.2"
}
],
"gene_symbol": "SPRED3",
"gene_hgnc_id": 31041,
"dbsnp": "rs780141379",
"frequency_reference_population": 0.0000065927015,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000659371,
"gnomad_genomes_af": 0.00000658467,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2548799216747284,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.7459999918937683,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.404,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1156,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.14,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.064,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.23,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": 0.949602962577552,
"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_001042522.3",
"gene_symbol": "SPRED3",
"hgnc_id": 31041,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.176A>G",
"hgvs_p": "p.Lys59Arg"
}
],
"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
}