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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: 16-28981548-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=28981548&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 28981548,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_032038.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "c.742C>T",
"hgvs_p": "p.Arg248Cys",
"transcript": "NM_032038.3",
"protein_id": "NP_114427.1",
"transcript_support_level": null,
"aa_start": 248,
"aa_end": null,
"aa_length": 528,
"cds_start": 742,
"cds_end": null,
"cds_length": 1587,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000311008.16",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032038.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "c.742C>T",
"hgvs_p": "p.Arg248Cys",
"transcript": "ENST00000311008.16",
"protein_id": "ENSP00000309945.11",
"transcript_support_level": 1,
"aa_start": 248,
"aa_end": null,
"aa_length": 528,
"cds_start": 742,
"cds_end": null,
"cds_length": 1587,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_032038.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000311008.16"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "c.877C>T",
"hgvs_p": "p.Arg293Cys",
"transcript": "ENST00000565975.5",
"protein_id": "ENSP00000454360.1",
"transcript_support_level": 1,
"aa_start": 293,
"aa_end": null,
"aa_length": 573,
"cds_start": 877,
"cds_end": null,
"cds_length": 1722,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000565975.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "c.742C>T",
"hgvs_p": "p.Arg248Cys",
"transcript": "ENST00000334536.12",
"protein_id": "ENSP00000335494.8",
"transcript_support_level": 1,
"aa_start": 248,
"aa_end": null,
"aa_length": 476,
"cds_start": 742,
"cds_end": null,
"cds_length": 1431,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000334536.12"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "c.676C>T",
"hgvs_p": "p.Arg226Cys",
"transcript": "ENST00000352260.11",
"protein_id": "ENSP00000306050.10",
"transcript_support_level": 1,
"aa_start": 226,
"aa_end": null,
"aa_length": 454,
"cds_start": 676,
"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": "ENST00000352260.11"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "c.724C>T",
"hgvs_p": "p.Arg242Cys",
"transcript": "ENST00000566059.5",
"protein_id": "ENSP00000456119.1",
"transcript_support_level": 5,
"aa_start": 242,
"aa_end": null,
"aa_length": 537,
"cds_start": 724,
"cds_end": null,
"cds_length": 1615,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000566059.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "c.742C>T",
"hgvs_p": "p.Arg248Cys",
"transcript": "NM_001142448.2",
"protein_id": "NP_001135920.1",
"transcript_support_level": null,
"aa_start": 248,
"aa_end": null,
"aa_length": 528,
"cds_start": 742,
"cds_end": null,
"cds_length": 1587,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001142448.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "c.742C>T",
"hgvs_p": "p.Arg248Cys",
"transcript": "NM_001142451.2",
"protein_id": "NP_001135923.1",
"transcript_support_level": null,
"aa_start": 248,
"aa_end": null,
"aa_length": 476,
"cds_start": 742,
"cds_end": null,
"cds_length": 1431,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001142451.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "c.523C>T",
"hgvs_p": "p.Arg175Cys",
"transcript": "NM_001142450.2",
"protein_id": "NP_001135922.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 455,
"cds_start": 523,
"cds_end": null,
"cds_length": 1368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001142450.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "c.523C>T",
"hgvs_p": "p.Arg175Cys",
"transcript": "ENST00000323081.12",
"protein_id": "ENSP00000318228.8",
"transcript_support_level": 2,
"aa_start": 175,
"aa_end": null,
"aa_length": 455,
"cds_start": 523,
"cds_end": null,
"cds_length": 1368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000323081.12"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "c.676C>T",
"hgvs_p": "p.Arg226Cys",
"transcript": "NM_001142449.2",
"protein_id": "NP_001135921.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 454,
"cds_start": 676,
"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": "NM_001142449.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "c.877C>T",
"hgvs_p": "p.Arg293Cys",
"transcript": "XM_047434739.1",
"protein_id": "XP_047290695.1",
"transcript_support_level": null,
"aa_start": 293,
"aa_end": null,
"aa_length": 586,
"cds_start": 877,
"cds_end": null,
"cds_length": 1761,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434739.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "c.790C>T",
"hgvs_p": "p.Arg264Cys",
"transcript": "XM_047434740.1",
"protein_id": "XP_047290696.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 544,
"cds_start": 790,
"cds_end": null,
"cds_length": 1635,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434740.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "c.877C>T",
"hgvs_p": "p.Arg293Cys",
"transcript": "XM_006721096.5",
"protein_id": "XP_006721159.1",
"transcript_support_level": null,
"aa_start": 293,
"aa_end": null,
"aa_length": 521,
"cds_start": 877,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006721096.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "c.877C>T",
"hgvs_p": "p.Arg293Cys",
"transcript": "XM_047434741.1",
"protein_id": "XP_047290697.1",
"transcript_support_level": null,
"aa_start": 293,
"aa_end": null,
"aa_length": 487,
"cds_start": 877,
"cds_end": null,
"cds_length": 1464,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434741.1"
},
{
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "c.615+2077C>T",
"hgvs_p": null,
"transcript": "ENST00000564476.1",
"protein_id": "ENSP00000455429.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 273,
"cds_start": null,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000564476.1"
},
{
"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": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "c.106-1309C>T",
"hgvs_p": null,
"transcript": "ENST00000568829.1",
"protein_id": "ENSP00000455467.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 178,
"cds_start": null,
"cds_end": null,
"cds_length": 537,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000568829.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"hgvs_c": "n.354C>T",
"hgvs_p": null,
"transcript": "ENST00000561868.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000561868.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000261067",
"gene_hgnc_id": null,
"hgvs_c": "n.1007C>T",
"hgvs_p": null,
"transcript": "ENST00000569969.5",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000569969.5"
}
],
"gene_symbol": "SPNS1",
"gene_hgnc_id": 30621,
"dbsnp": "rs752225271",
"frequency_reference_population": 0.00001548989,
"hom_count_reference_population": 0,
"allele_count_reference_population": 25,
"gnomad_exomes_af": 0.0000164179,
"gnomad_genomes_af": 0.00000657298,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.30480891466140747,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.28,
"revel_prediction": "Benign",
"alphamissense_score": 0.2767,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.23,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.986,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_032038.3",
"gene_symbol": "SPNS1",
"hgnc_id": 30621,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.742C>T",
"hgvs_p": "p.Arg248Cys"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000569969.5",
"gene_symbol": "ENSG00000261067",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1007C>T",
"hgvs_p": null
}
],
"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
}