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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: 15-50908845-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=50908845&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "AP4E1",
"hgnc_id": 573,
"hgvs_c": "c.67G>A",
"hgvs_p": "p.Gly23Ser",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_007347.5",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "ENSG00000273674",
"hgnc_id": null,
"hgvs_c": "n.-246C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "ENST00000613161.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 3,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0742,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.45,
"chr": "15",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Spastic paraplegia",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.11928364634513855,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1137,
"aa_ref": "G",
"aa_start": 23,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6743,
"cdna_start": 163,
"cds_end": null,
"cds_length": 3414,
"cds_start": 67,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_007347.5",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.67G>A",
"hgvs_p": "p.Gly23Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000261842.10",
"protein_coding": true,
"protein_id": "NP_031373.2",
"strand": true,
"transcript": "NM_007347.5",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1137,
"aa_ref": "G",
"aa_start": 23,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6743,
"cdna_start": 163,
"cds_end": null,
"cds_length": 3414,
"cds_start": 67,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000261842.10",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.67G>A",
"hgvs_p": "p.Gly23Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_007347.5",
"protein_coding": true,
"protein_id": "ENSP00000261842.5",
"strand": true,
"transcript": "ENST00000261842.10",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1062,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6653,
"cdna_start": null,
"cds_end": null,
"cds_length": 3189,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 21,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000560508.1",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.-182G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000452976.1",
"strand": true,
"transcript": "ENST00000560508.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 4165,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 21,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000558439.5",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "n.67G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000452712.1",
"strand": true,
"transcript": "ENST00000558439.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 4024,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 20,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000561393.5",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "n.-182G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000452711.1",
"strand": true,
"transcript": "ENST00000561393.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 4024,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 20,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000561393.5",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "n.-182G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000452711.1",
"strand": true,
"transcript": "ENST00000561393.5",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1036,
"aa_ref": "G",
"aa_start": 23,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3277,
"cdna_start": 160,
"cds_end": null,
"cds_length": 3111,
"cds_start": 67,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000879007.1",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.67G>A",
"hgvs_p": "p.Gly23Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549066.1",
"strand": true,
"transcript": "ENST00000879007.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1062,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6766,
"cdna_start": null,
"cds_end": null,
"cds_length": 3189,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 21,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001252127.2",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.-182G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001239056.1",
"strand": true,
"transcript": "NM_001252127.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1062,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7649,
"cdna_start": null,
"cds_end": null,
"cds_length": 3189,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_005254264.5",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.-76+202G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005254321.1",
"strand": true,
"transcript": "XM_005254264.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1603,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000561441.5",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "n.67G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000453112.1",
"strand": true,
"transcript": "ENST00000561441.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1062,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6932,
"cdna_start": null,
"cds_end": null,
"cds_length": 3189,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_006720447.5",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.-650G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006720510.1",
"strand": true,
"transcript": "XM_006720447.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1062,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6955,
"cdna_start": null,
"cds_end": null,
"cds_length": 3189,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047432325.1",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.-673G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288281.1",
"strand": true,
"transcript": "XM_047432325.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2398,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000613161.4",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000273674",
"hgvs_c": "n.-246C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000613161.4",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 990,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000655436.3",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000273674",
"hgvs_c": "n.-236C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000655436.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 972,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000656830.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000273674",
"hgvs_c": "n.-242C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000656830.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 562,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000693106.2",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000273674",
"hgvs_c": "n.-235C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000693106.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 847,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000841903.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000273674",
"hgvs_c": "n.-241C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000841903.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 853,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000841905.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000273674",
"hgvs_c": "n.-239C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000841905.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 159,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000841906.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000273674",
"hgvs_c": "n.-248C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000841906.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs373684336",
"effect": "missense_variant",
"frequency_reference_population": 0.0000018649897,
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.86645e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131378,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Spastic paraplegia",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.851,
"pos": 50908845,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.016,
"splice_prediction_selected": "Uncertain_significance",
"splice_score_selected": 0.38999998569488525,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Uncertain_significance",
"spliceai_max_score": 0.39,
"transcript": "NM_007347.5"
}
]
}