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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: 5-148088587-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=148088587&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 148088587,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_006846.4",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK5",
"gene_hgnc_id": 15464,
"hgvs_c": "c.456G>A",
"hgvs_p": "p.Lys152Lys",
"transcript": "NM_006846.4",
"protein_id": "NP_006837.2",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 1064,
"cds_start": 456,
"cds_end": null,
"cds_length": 3195,
"cdna_start": 521,
"cdna_end": null,
"cdna_length": 3651,
"mane_select": "ENST00000256084.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK5",
"gene_hgnc_id": 15464,
"hgvs_c": "c.456G>A",
"hgvs_p": "p.Lys152Lys",
"transcript": "ENST00000256084.8",
"protein_id": "ENSP00000256084.7",
"transcript_support_level": 1,
"aa_start": 152,
"aa_end": null,
"aa_length": 1064,
"cds_start": 456,
"cds_end": null,
"cds_length": 3195,
"cdna_start": 521,
"cdna_end": null,
"cdna_length": 3651,
"mane_select": "NM_006846.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK5",
"gene_hgnc_id": 15464,
"hgvs_c": "c.456G>A",
"hgvs_p": "p.Lys152Lys",
"transcript": "ENST00000359874.7",
"protein_id": "ENSP00000352936.3",
"transcript_support_level": 1,
"aa_start": 152,
"aa_end": null,
"aa_length": 1094,
"cds_start": 456,
"cds_end": null,
"cds_length": 3285,
"cdna_start": 529,
"cdna_end": null,
"cdna_length": 3656,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK5",
"gene_hgnc_id": 15464,
"hgvs_c": "c.456G>A",
"hgvs_p": "p.Lys152Lys",
"transcript": "ENST00000398454.5",
"protein_id": "ENSP00000381472.1",
"transcript_support_level": 1,
"aa_start": 152,
"aa_end": null,
"aa_length": 916,
"cds_start": 456,
"cds_end": null,
"cds_length": 2751,
"cdna_start": 529,
"cdna_end": null,
"cdna_length": 2915,
"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": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK5",
"gene_hgnc_id": 15464,
"hgvs_c": "n.456G>A",
"hgvs_p": null,
"transcript": "ENST00000476697.7",
"protein_id": "ENSP00000427943.1",
"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": 1073,
"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": 6,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK5",
"gene_hgnc_id": 15464,
"hgvs_c": "n.620G>A",
"hgvs_p": null,
"transcript": "ENST00000507988.5",
"protein_id": null,
"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": 2408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK5",
"gene_hgnc_id": 15464,
"hgvs_c": "c.456G>A",
"hgvs_p": "p.Lys152Lys",
"transcript": "NM_001127698.2",
"protein_id": "NP_001121170.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 1094,
"cds_start": 456,
"cds_end": null,
"cds_length": 3285,
"cdna_start": 521,
"cdna_end": null,
"cdna_length": 3741,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK5",
"gene_hgnc_id": 15464,
"hgvs_c": "c.456G>A",
"hgvs_p": "p.Lys152Lys",
"transcript": "NM_001127699.2",
"protein_id": "NP_001121171.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 916,
"cds_start": 456,
"cds_end": null,
"cds_length": 2751,
"cdna_start": 521,
"cdna_end": null,
"cdna_length": 2917,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK5",
"gene_hgnc_id": 15464,
"hgvs_c": "c.399G>A",
"hgvs_p": "p.Lys133Lys",
"transcript": "ENST00000508733.5",
"protein_id": "ENSP00000421519.1",
"transcript_support_level": 5,
"aa_start": 133,
"aa_end": null,
"aa_length": 868,
"cds_start": 399,
"cds_end": null,
"cds_length": 2609,
"cdna_start": 464,
"cdna_end": null,
"cdna_length": 2674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK5",
"gene_hgnc_id": 15464,
"hgvs_c": "c.399G>A",
"hgvs_p": "p.Lys133Lys",
"transcript": "XM_047416662.1",
"protein_id": "XP_047272618.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 1075,
"cds_start": 399,
"cds_end": null,
"cds_length": 3228,
"cdna_start": 464,
"cdna_end": null,
"cdna_length": 3684,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK5",
"gene_hgnc_id": 15464,
"hgvs_c": "c.372G>A",
"hgvs_p": "p.Lys124Lys",
"transcript": "XM_011537551.3",
"protein_id": "XP_011535853.1",
"transcript_support_level": null,
"aa_start": 124,
"aa_end": null,
"aa_length": 1066,
"cds_start": 372,
"cds_end": null,
"cds_length": 3201,
"cdna_start": 444,
"cdna_end": null,
"cdna_length": 3664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "FBXO38-DT",
"gene_hgnc_id": 55589,
"hgvs_c": "n.2634C>T",
"hgvs_p": null,
"transcript": "ENST00000667608.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2991,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FBXO38-DT",
"gene_hgnc_id": 55589,
"hgvs_c": "n.1560C>T",
"hgvs_p": null,
"transcript": "ENST00000671159.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2022,
"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": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPINK5",
"gene_hgnc_id": 15464,
"hgvs_c": "n.326G>A",
"hgvs_p": null,
"transcript": "ENST00000698105.1",
"protein_id": null,
"transcript_support_level": null,
"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": 878,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124901185",
"gene_hgnc_id": null,
"hgvs_c": "n.1560C>T",
"hgvs_p": null,
"transcript": "XR_007059138.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1983,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LOC124901185",
"gene_hgnc_id": null,
"hgvs_c": "n.611+767C>T",
"hgvs_p": null,
"transcript": "XR_007059139.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1122,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SPINK5",
"gene_hgnc_id": 15464,
"dbsnp": "rs777350307",
"frequency_reference_population": 0.00014396025,
"hom_count_reference_population": 0,
"allele_count_reference_population": 232,
"gnomad_exomes_af": 0.000149332,
"gnomad_genomes_af": 0.0000922765,
"gnomad_exomes_ac": 218,
"gnomad_genomes_ac": 14,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7599999904632568,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.76,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.159,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Benign",
"transcript": "NM_006846.4",
"gene_symbol": "SPINK5",
"hgnc_id": 15464,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.456G>A",
"hgvs_p": "p.Lys152Lys"
},
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000667608.1",
"gene_symbol": "FBXO38-DT",
"hgnc_id": 55589,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.2634C>T",
"hgvs_p": null
},
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "XR_007059138.1",
"gene_symbol": "LOC124901185",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1560C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Ichthyosis linearis circumflexa",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Ichthyosis linearis circumflexa",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}