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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: 19-48629377-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=48629377&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 48629377,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000245222.9",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHK2",
"gene_hgnc_id": 18859,
"hgvs_c": "c.1569G>A",
"hgvs_p": "p.Leu523Leu",
"transcript": "NM_020126.5",
"protein_id": "NP_064511.2",
"transcript_support_level": null,
"aa_start": 523,
"aa_end": null,
"aa_length": 654,
"cds_start": 1569,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 1720,
"cdna_end": null,
"cdna_length": 2748,
"mane_select": "ENST00000245222.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHK2",
"gene_hgnc_id": 18859,
"hgvs_c": "c.1569G>A",
"hgvs_p": "p.Leu523Leu",
"transcript": "ENST00000245222.9",
"protein_id": "ENSP00000245222.3",
"transcript_support_level": 1,
"aa_start": 523,
"aa_end": null,
"aa_length": 654,
"cds_start": 1569,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 1720,
"cdna_end": null,
"cdna_length": 2748,
"mane_select": "NM_020126.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHK2",
"gene_hgnc_id": 18859,
"hgvs_c": "c.1461G>A",
"hgvs_p": "p.Leu487Leu",
"transcript": "ENST00000599029.2",
"protein_id": "ENSP00000472983.1",
"transcript_support_level": 1,
"aa_start": 487,
"aa_end": null,
"aa_length": 663,
"cds_start": 1461,
"cds_end": null,
"cds_length": 1992,
"cdna_start": 2452,
"cdna_end": null,
"cdna_length": 3085,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHK2",
"gene_hgnc_id": 18859,
"hgvs_c": "c.1569G>A",
"hgvs_p": "p.Leu523Leu",
"transcript": "ENST00000598088.5",
"protein_id": "ENSP00000469158.1",
"transcript_support_level": 1,
"aa_start": 523,
"aa_end": null,
"aa_length": 654,
"cds_start": 1569,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 1838,
"cdna_end": null,
"cdna_length": 2866,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHK2",
"gene_hgnc_id": 18859,
"hgvs_c": "c.1461G>A",
"hgvs_p": "p.Leu487Leu",
"transcript": "ENST00000599748.5",
"protein_id": "ENSP00000471205.1",
"transcript_support_level": 1,
"aa_start": 487,
"aa_end": null,
"aa_length": 618,
"cds_start": 1461,
"cds_end": null,
"cds_length": 1857,
"cdna_start": 1655,
"cdna_end": null,
"cdna_length": 2683,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHK2",
"gene_hgnc_id": 18859,
"hgvs_c": "n.*947G>A",
"hgvs_p": null,
"transcript": "ENST00000426514.2",
"protein_id": "ENSP00000410044.2",
"transcript_support_level": 1,
"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": 1493,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHK2",
"gene_hgnc_id": 18859,
"hgvs_c": "n.*947G>A",
"hgvs_p": null,
"transcript": "ENST00000426514.2",
"protein_id": "ENSP00000410044.2",
"transcript_support_level": 1,
"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": 1493,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHK2",
"gene_hgnc_id": 18859,
"hgvs_c": "c.1569G>A",
"hgvs_p": "p.Leu523Leu",
"transcript": "NM_001204159.3",
"protein_id": "NP_001191088.1",
"transcript_support_level": null,
"aa_start": 523,
"aa_end": null,
"aa_length": 654,
"cds_start": 1569,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 1866,
"cdna_end": null,
"cdna_length": 2894,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHK2",
"gene_hgnc_id": 18859,
"hgvs_c": "c.1461G>A",
"hgvs_p": "p.Leu487Leu",
"transcript": "NM_001204160.3",
"protein_id": "NP_001191089.1",
"transcript_support_level": null,
"aa_start": 487,
"aa_end": null,
"aa_length": 618,
"cds_start": 1461,
"cds_end": null,
"cds_length": 1857,
"cdna_start": 1578,
"cdna_end": null,
"cdna_length": 2606,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHK2",
"gene_hgnc_id": 18859,
"hgvs_c": "c.1392G>A",
"hgvs_p": "p.Leu464Leu",
"transcript": "NM_001204158.3",
"protein_id": "NP_001191087.1",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 595,
"cds_start": 1392,
"cds_end": null,
"cds_length": 1788,
"cdna_start": 1543,
"cdna_end": null,
"cdna_length": 2571,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHK2",
"gene_hgnc_id": 18859,
"hgvs_c": "c.1392G>A",
"hgvs_p": "p.Leu464Leu",
"transcript": "ENST00000600537.5",
"protein_id": "ENSP00000470092.1",
"transcript_support_level": 2,
"aa_start": 464,
"aa_end": null,
"aa_length": 595,
"cds_start": 1392,
"cds_end": null,
"cds_length": 1788,
"cdna_start": 1597,
"cdna_end": null,
"cdna_length": 2136,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHK2",
"gene_hgnc_id": 18859,
"hgvs_c": "c.951G>A",
"hgvs_p": "p.Leu317Leu",
"transcript": "NM_001243876.2",
"protein_id": "NP_001230805.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 448,
"cds_start": 951,
"cds_end": null,
"cds_length": 1347,
"cdna_start": 1248,
"cdna_end": null,
"cdna_length": 2276,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPHK2",
"gene_hgnc_id": 18859,
"hgvs_c": "c.951G>A",
"hgvs_p": "p.Leu317Leu",
"transcript": "ENST00000340932.7",
"protein_id": "ENSP00000341091.4",
"transcript_support_level": 5,
"aa_start": 317,
"aa_end": null,
"aa_length": 448,
"cds_start": 951,
"cds_end": null,
"cds_length": 1347,
"cdna_start": 1463,
"cdna_end": null,
"cdna_length": 2492,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank_end": null,
"gene_symbol": "SPHK2",
"gene_hgnc_id": 18859,
"hgvs_c": "n.765-1057G>A",
"hgvs_p": null,
"transcript": "ENST00000597434.5",
"protein_id": "ENSP00000471111.1",
"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": 1542,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SPHK2",
"gene_hgnc_id": 18859,
"dbsnp": "rs3745733",
"frequency_reference_population": 0.12821348,
"hom_count_reference_population": 14115,
"allele_count_reference_population": 206645,
"gnomad_exomes_af": 0.1301,
"gnomad_genomes_af": 0.110132,
"gnomad_exomes_ac": 189873,
"gnomad_genomes_ac": 16772,
"gnomad_exomes_homalt": 12970,
"gnomad_genomes_homalt": 1145,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5799999833106995,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.085,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000245222.9",
"gene_symbol": "SPHK2",
"hgnc_id": 18859,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1569G>A",
"hgvs_p": "p.Leu523Leu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}