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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: X-153807337-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153807337&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153807337,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001303512.2",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.347C>T",
"hgvs_p": "p.Ala116Val",
"transcript": "NM_001303512.2",
"protein_id": "NP_001290441.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 775,
"cds_start": 347,
"cds_end": null,
"cds_length": 2328,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000393758.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303512.2"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.347C>T",
"hgvs_p": "p.Ala116Val",
"transcript": "ENST00000393758.7",
"protein_id": "ENSP00000377355.3",
"transcript_support_level": 1,
"aa_start": 116,
"aa_end": null,
"aa_length": 775,
"cds_start": 347,
"cds_end": null,
"cds_length": 2328,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001303512.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000393758.7"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.329C>T",
"hgvs_p": "p.Ala110Val",
"transcript": "ENST00000164640.8",
"protein_id": "ENSP00000164640.4",
"transcript_support_level": 1,
"aa_start": 110,
"aa_end": null,
"aa_length": 769,
"cds_start": 329,
"cds_end": null,
"cds_length": 2310,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000164640.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.61-497C>T",
"hgvs_p": null,
"transcript": "ENST00000544474.5",
"protein_id": "ENSP00000442033.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 660,
"cds_start": null,
"cds_end": null,
"cds_length": 1983,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000544474.5"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.347C>T",
"hgvs_p": "p.Ala116Val",
"transcript": "ENST00000933007.1",
"protein_id": "ENSP00000603066.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 774,
"cds_start": 347,
"cds_end": null,
"cds_length": 2325,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933007.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.329C>T",
"hgvs_p": "p.Ala110Val",
"transcript": "NM_032512.5",
"protein_id": "NP_115901.2",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 769,
"cds_start": 329,
"cds_end": null,
"cds_length": 2310,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032512.5"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.104C>T",
"hgvs_p": "p.Ala35Val",
"transcript": "NM_001303515.2",
"protein_id": "NP_001290444.1",
"transcript_support_level": null,
"aa_start": 35,
"aa_end": null,
"aa_length": 694,
"cds_start": 104,
"cds_end": null,
"cds_length": 2085,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303515.2"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.86C>T",
"hgvs_p": "p.Ala29Val",
"transcript": "NM_001303516.2",
"protein_id": "NP_001290445.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 688,
"cds_start": 86,
"cds_end": null,
"cds_length": 2067,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303516.2"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.41C>T",
"hgvs_p": "p.Ala14Val",
"transcript": "NM_001303513.3",
"protein_id": "NP_001290442.1",
"transcript_support_level": null,
"aa_start": 14,
"aa_end": null,
"aa_length": 673,
"cds_start": 41,
"cds_end": null,
"cds_length": 2022,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303513.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.145-497C>T",
"hgvs_p": null,
"transcript": "ENST00000933008.1",
"protein_id": "ENSP00000603067.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 688,
"cds_start": null,
"cds_end": null,
"cds_length": 2067,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933008.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.61-497C>T",
"hgvs_p": null,
"transcript": "NM_001303514.2",
"protein_id": "NP_001290443.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 660,
"cds_start": null,
"cds_end": null,
"cds_length": 1983,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001303514.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "c.61-1204C>T",
"hgvs_p": null,
"transcript": "ENST00000933009.1",
"protein_id": "ENSP00000603068.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 627,
"cds_start": null,
"cds_end": null,
"cds_length": 1884,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933009.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "n.655C>T",
"hgvs_p": null,
"transcript": "ENST00000468491.1",
"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": "ENST00000468491.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "n.393C>T",
"hgvs_p": null,
"transcript": "ENST00000475140.5",
"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": "ENST00000475140.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "n.*221C>T",
"hgvs_p": null,
"transcript": "ENST00000480650.3",
"protein_id": "ENSP00000476940.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000480650.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "n.547C>T",
"hgvs_p": null,
"transcript": "ENST00000483693.5",
"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": "ENST00000483693.5"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "n.322C>T",
"hgvs_p": null,
"transcript": "ENST00000484792.5",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000484792.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "n.*221C>T",
"hgvs_p": null,
"transcript": "ENST00000480650.3",
"protein_id": "ENSP00000476940.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000480650.3"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"hgvs_c": "n.328-497C>T",
"hgvs_p": null,
"transcript": "ENST00000480418.5",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000480418.5"
}
],
"gene_symbol": "PDZD4",
"gene_hgnc_id": 21167,
"dbsnp": "rs368296370",
"frequency_reference_population": 0.000005792832,
"hom_count_reference_population": 1,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.00000456386,
"gnomad_genomes_af": 0.0000177264,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07194489240646362,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.039,
"revel_prediction": "Benign",
"alphamissense_score": 0.0998,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.69,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.121,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001303512.2",
"gene_symbol": "PDZD4",
"hgnc_id": 21167,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.347C>T",
"hgvs_p": "p.Ala116Val"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}