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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: 6-41784980-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=41784980&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PRICKLE4",
"hgnc_id": 16805,
"hgvs_c": "c.286C>A",
"hgvs_p": "p.Gln96Lys",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_013397.6",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000124593",
"hgnc_id": null,
"hgvs_c": "n.286C>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000335515.10",
"verdict": "Likely_benign"
},
{
"benign_score": 8,
"criteria": [
"BP4_Strong",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "FRS3",
"hgnc_id": 16970,
"hgvs_c": "c.-168+2480G>T",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -8,
"transcript": "ENST00000957913.1",
"verdict": "Benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 34,
"alphamissense_prediction": null,
"alphamissense_score": 0.1004,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.44,
"chr": "6",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.04969707131385803,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 384,
"aa_ref": "Q",
"aa_start": 96,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1706,
"cdna_start": 514,
"cds_end": null,
"cds_length": 1155,
"cds_start": 286,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_013397.6",
"gene_hgnc_id": 16805,
"gene_symbol": "PRICKLE4",
"hgvs_c": "c.286C>A",
"hgvs_p": "p.Gln96Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000458694.6",
"protein_coding": true,
"protein_id": "NP_037529.3",
"strand": true,
"transcript": "NM_013397.6",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 384,
"aa_ref": "Q",
"aa_start": 96,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1706,
"cdna_start": 514,
"cds_end": null,
"cds_length": 1155,
"cds_start": 286,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000458694.6",
"gene_hgnc_id": 16805,
"gene_symbol": "PRICKLE4",
"hgvs_c": "c.286C>A",
"hgvs_p": "p.Gln96Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_013397.6",
"protein_coding": true,
"protein_id": "ENSP00000404911.1",
"strand": true,
"transcript": "ENST00000458694.6",
"transcript_support_level": 5
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 344,
"aa_ref": "Q",
"aa_start": 56,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2098,
"cdna_start": 986,
"cds_end": null,
"cds_length": 1035,
"cds_start": 166,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000359201.6",
"gene_hgnc_id": 16805,
"gene_symbol": "PRICKLE4",
"hgvs_c": "c.166C>A",
"hgvs_p": "p.Gln56Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000352128.6",
"strand": true,
"transcript": "ENST00000359201.6",
"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": 2871,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000335515.10",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000124593",
"hgvs_c": "n.286C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000335185.6",
"strand": true,
"transcript": "ENST00000335515.10",
"transcript_support_level": 2
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 384,
"aa_ref": "Q",
"aa_start": 96,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1605,
"cdna_start": 423,
"cds_end": null,
"cds_length": 1155,
"cds_start": 286,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000938055.1",
"gene_hgnc_id": 16805,
"gene_symbol": "PRICKLE4",
"hgvs_c": "c.286C>A",
"hgvs_p": "p.Gln96Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000608114.1",
"strand": true,
"transcript": "ENST00000938055.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 344,
"aa_ref": "Q",
"aa_start": 56,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1035,
"cdna_start": 166,
"cds_end": null,
"cds_length": 1035,
"cds_start": 166,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000394260.2",
"gene_hgnc_id": 16805,
"gene_symbol": "PRICKLE4",
"hgvs_c": "c.166C>A",
"hgvs_p": "p.Gln56Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000377803.1",
"strand": true,
"transcript": "ENST00000394260.2",
"transcript_support_level": 2
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 312,
"aa_ref": "Q",
"aa_start": 56,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 939,
"cdna_start": 166,
"cds_end": null,
"cds_length": 939,
"cds_start": 166,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000394259.5",
"gene_hgnc_id": 16805,
"gene_symbol": "PRICKLE4",
"hgvs_c": "c.166C>A",
"hgvs_p": "p.Gln56Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000377802.1",
"strand": true,
"transcript": "ENST00000394259.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 492,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2200,
"cdna_start": null,
"cds_end": null,
"cds_length": 1479,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000957913.1",
"gene_hgnc_id": 16970,
"gene_symbol": "FRS3",
"hgvs_c": "c.-168+2480G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627972.1",
"strand": false,
"transcript": "ENST00000957913.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 35,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 326,
"cdna_start": null,
"cds_end": null,
"cds_length": 109,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000422888.5",
"gene_hgnc_id": 16970,
"gene_symbol": "FRS3",
"hgvs_c": "c.-168+1513G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000413214.1",
"strand": false,
"transcript": "ENST00000422888.5",
"transcript_support_level": 5
},
{
"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": 3947,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000456057.5",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000124593",
"hgvs_c": "n.*470C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000389023.1",
"strand": true,
"transcript": "ENST00000456057.5",
"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": 366,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000463606.1",
"gene_hgnc_id": 16805,
"gene_symbol": "PRICKLE4",
"hgvs_c": "n.189C>A",
"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": "ENST00000463606.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3043,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000487182.5",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000124593",
"hgvs_c": "n.1049C>A",
"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": "ENST00000487182.5",
"transcript_support_level": 2
},
{
"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": 3947,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000456057.5",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000124593",
"hgvs_c": "n.*470C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000389023.1",
"strand": true,
"transcript": "ENST00000456057.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 280,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 880,
"cdna_start": null,
"cds_end": null,
"cds_length": 843,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000483200.2",
"gene_hgnc_id": 16805,
"gene_symbol": "PRICKLE4",
"hgvs_c": "c.-27C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000489132.1",
"strand": true,
"transcript": "ENST00000483200.2",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs376424716",
"effect": "missense_variant",
"frequency_reference_population": 0.000021066511,
"gene_hgnc_id": 16805,
"gene_symbol": "PRICKLE4",
"gnomad_exomes_ac": 25,
"gnomad_exomes_af": 0.0000171032,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 9,
"gnomad_genomes_af": 0.0000591242,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.139,
"pos": 41784980,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.127,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.07000000029802322,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.07,
"transcript": "NM_013397.6"
}
]
}