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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: 3-150972652-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=150972652&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 150972652,
"ref": "T",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000327047.6",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLRN1",
"gene_hgnc_id": 12605,
"hgvs_c": "c.57A>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "NM_174878.3",
"protein_id": "NP_777367.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 232,
"cds_start": 57,
"cds_end": null,
"cds_length": 699,
"cdna_start": 76,
"cdna_end": null,
"cdna_length": 2087,
"mane_select": "ENST00000327047.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLRN1",
"gene_hgnc_id": 12605,
"hgvs_c": "c.57A>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "ENST00000327047.6",
"protein_id": "ENSP00000322280.1",
"transcript_support_level": 1,
"aa_start": 19,
"aa_end": null,
"aa_length": 232,
"cds_start": 57,
"cds_end": null,
"cds_length": 699,
"cdna_start": 76,
"cdna_end": null,
"cdna_length": 2087,
"mane_select": "NM_174878.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLRN1",
"gene_hgnc_id": 12605,
"hgvs_c": "c.57A>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "ENST00000328863.8",
"protein_id": "ENSP00000329158.4",
"transcript_support_level": 1,
"aa_start": 19,
"aa_end": null,
"aa_length": 245,
"cds_start": 57,
"cds_end": null,
"cds_length": 738,
"cdna_start": 57,
"cdna_end": null,
"cdna_length": 738,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLRN1",
"gene_hgnc_id": 12605,
"hgvs_c": "c.57A>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "NM_001195794.1",
"protein_id": "NP_001182723.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 245,
"cds_start": 57,
"cds_end": null,
"cds_length": 738,
"cdna_start": 348,
"cdna_end": null,
"cdna_length": 2398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLRN1",
"gene_hgnc_id": 12605,
"hgvs_c": "c.57A>T",
"hgvs_p": "p.Ala19Ala",
"transcript": "NM_001256819.2",
"protein_id": "NP_001243748.1",
"transcript_support_level": null,
"aa_start": 19,
"aa_end": null,
"aa_length": 185,
"cds_start": 57,
"cds_end": null,
"cds_length": 558,
"cdna_start": 76,
"cdna_end": null,
"cdna_length": 2259,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLRN1",
"gene_hgnc_id": 12605,
"hgvs_c": "c.33A>T",
"hgvs_p": "p.Ala11Ala",
"transcript": "ENST00000468836.2",
"protein_id": "ENSP00000419892.2",
"transcript_support_level": 3,
"aa_start": 11,
"aa_end": null,
"aa_length": 177,
"cds_start": 33,
"cds_end": null,
"cds_length": 534,
"cdna_start": 33,
"cdna_end": null,
"cdna_length": 722,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLRN1",
"gene_hgnc_id": 12605,
"hgvs_c": "n.63A>T",
"hgvs_p": null,
"transcript": "ENST00000472224.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 606,
"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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLRN1",
"gene_hgnc_id": 12605,
"hgvs_c": "n.76A>T",
"hgvs_p": null,
"transcript": "NR_046380.3",
"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": 2277,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000243273",
"gene_hgnc_id": null,
"hgvs_c": "n.236-28922T>A",
"hgvs_p": null,
"transcript": "ENST00000469268.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 565,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SIAH2-AS1",
"gene_hgnc_id": 40526,
"hgvs_c": "n.124-90274T>A",
"hgvs_p": null,
"transcript": "ENST00000476886.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 2223,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SIAH2-AS1",
"gene_hgnc_id": 40526,
"hgvs_c": "n.447-81210T>A",
"hgvs_p": null,
"transcript": "ENST00000716210.1",
"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": 865,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIAH2-AS1",
"gene_hgnc_id": 40526,
"hgvs_c": "n.-26T>A",
"hgvs_p": null,
"transcript": "ENST00000465576.1",
"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": 2045,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLRN1",
"gene_hgnc_id": 12605,
"hgvs_c": "n.-103A>T",
"hgvs_p": null,
"transcript": "ENST00000644099.1",
"protein_id": "ENSP00000494762.1",
"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": 464,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLRN1",
"gene_hgnc_id": 12605,
"hgvs_c": "n.-103A>T",
"hgvs_p": null,
"transcript": "ENST00000645441.1",
"protein_id": "ENSP00000496637.1",
"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": 468,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLRN1-AS1",
"gene_hgnc_id": 30895,
"hgvs_c": "n.-26T>A",
"hgvs_p": null,
"transcript": "NR_024066.2",
"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": 2941,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CLRN1",
"gene_hgnc_id": 12605,
"dbsnp": "rs3796242",
"frequency_reference_population": 0.12303419,
"hom_count_reference_population": 13042,
"allele_count_reference_population": 198588,
"gnomad_exomes_af": 0.123037,
"gnomad_genomes_af": 0.123004,
"gnomad_exomes_ac": 179866,
"gnomad_genomes_ac": 18722,
"gnomad_exomes_homalt": 11749,
"gnomad_genomes_homalt": 1293,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6600000262260437,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.66,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.79,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000327047.6",
"gene_symbol": "CLRN1",
"hgnc_id": 12605,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.57A>T",
"hgvs_p": "p.Ala19Ala"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000476886.5",
"gene_symbol": "SIAH2-AS1",
"hgnc_id": 40526,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.124-90274T>A",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000469268.1",
"gene_symbol": "ENSG00000243273",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.236-28922T>A",
"hgvs_p": null
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NR_024066.2",
"gene_symbol": "CLRN1-AS1",
"hgnc_id": 30895,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-26T>A",
"hgvs_p": null
}
],
"clinvar_disease": "Retinal dystrophy,Usher syndrome type 3,Usher syndrome type 3A,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:8",
"phenotype_combined": "not specified|Usher syndrome type 3|Usher syndrome type 3A|not provided|Retinal dystrophy",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}