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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: 12-93850180-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=93850180&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 93850180,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_003805.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRADD",
"gene_hgnc_id": 2340,
"hgvs_c": "c.509G>A",
"hgvs_p": "p.Arg170His",
"transcript": "NM_003805.5",
"protein_id": "NP_003796.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 199,
"cds_start": 509,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000332896.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003805.5"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRADD",
"gene_hgnc_id": 2340,
"hgvs_c": "c.509G>A",
"hgvs_p": "p.Arg170His",
"transcript": "ENST00000332896.8",
"protein_id": "ENSP00000327647.3",
"transcript_support_level": 1,
"aa_start": 170,
"aa_end": null,
"aa_length": 199,
"cds_start": 509,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003805.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000332896.8"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRADD",
"gene_hgnc_id": 2340,
"hgvs_c": "c.509G>A",
"hgvs_p": "p.Arg170His",
"transcript": "ENST00000542893.2",
"protein_id": "ENSP00000439068.2",
"transcript_support_level": 1,
"aa_start": 170,
"aa_end": null,
"aa_length": 199,
"cds_start": 509,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000542893.2"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRADD",
"gene_hgnc_id": 2340,
"hgvs_c": "c.509G>A",
"hgvs_p": "p.Arg170His",
"transcript": "NM_001320099.2",
"protein_id": "NP_001307028.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 199,
"cds_start": 509,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001320099.2"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRADD",
"gene_hgnc_id": 2340,
"hgvs_c": "c.509G>A",
"hgvs_p": "p.Arg170His",
"transcript": "ENST00000880420.1",
"protein_id": "ENSP00000550479.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 199,
"cds_start": 509,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000880420.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRADD",
"gene_hgnc_id": 2340,
"hgvs_c": "c.509G>A",
"hgvs_p": "p.Arg170His",
"transcript": "ENST00000918988.1",
"protein_id": "ENSP00000589047.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 199,
"cds_start": 509,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918988.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CRADD",
"gene_hgnc_id": 2340,
"hgvs_c": "c.299-43870G>A",
"hgvs_p": null,
"transcript": "NM_001320100.2",
"protein_id": "NP_001307029.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 121,
"cds_start": null,
"cds_end": null,
"cds_length": 366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001320100.2"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CRADD",
"gene_hgnc_id": 2340,
"hgvs_c": "c.299-43870G>A",
"hgvs_p": null,
"transcript": "ENST00000548483.5",
"protein_id": "ENSP00000448685.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 121,
"cds_start": null,
"cds_end": null,
"cds_length": 366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000548483.5"
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CRADD",
"gene_hgnc_id": 2340,
"hgvs_c": "c.299-9139G>A",
"hgvs_p": null,
"transcript": "XM_047429805.1",
"protein_id": "XP_047285761.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 103,
"cds_start": null,
"cds_end": null,
"cds_length": 312,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047429805.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRADD",
"gene_hgnc_id": 2340,
"hgvs_c": "n.894G>A",
"hgvs_p": null,
"transcript": "ENST00000548330.1",
"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": "ENST00000548330.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRADD",
"gene_hgnc_id": 2340,
"hgvs_c": "n.309G>A",
"hgvs_p": null,
"transcript": "ENST00000550030.1",
"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": "ENST00000550030.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRADD",
"gene_hgnc_id": 2340,
"hgvs_c": "n.285G>A",
"hgvs_p": null,
"transcript": "ENST00000609189.1",
"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": "ENST00000609189.1"
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CRADD",
"gene_hgnc_id": 2340,
"hgvs_c": "n.299-9139G>A",
"hgvs_p": null,
"transcript": "ENST00000551065.5",
"protein_id": "ENSP00000448425.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000551065.5"
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CRADD",
"gene_hgnc_id": 2340,
"hgvs_c": "n.403-9139G>A",
"hgvs_p": null,
"transcript": "NR_135147.2",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_135147.2"
}
],
"gene_symbol": "CRADD",
"gene_hgnc_id": 2340,
"dbsnp": "rs141179774",
"frequency_reference_population": 0.00027390267,
"hom_count_reference_population": 0,
"allele_count_reference_population": 442,
"gnomad_exomes_af": 0.000251127,
"gnomad_genomes_af": 0.000492456,
"gnomad_exomes_ac": 367,
"gnomad_genomes_ac": 75,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00955238938331604,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.589,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0823,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.14,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.247,
"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": 15,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM2,PM5,PP5_Very_Strong,BP4",
"acmg_by_gene": [
{
"score": 15,
"benign_score": 1,
"pathogenic_score": 16,
"criteria": [
"PS3",
"PM2",
"PM5",
"PP5_Very_Strong",
"BP4"
],
"verdict": "Pathogenic",
"transcript": "NM_003805.5",
"gene_symbol": "CRADD",
"hgnc_id": 2340,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.509G>A",
"hgvs_p": "p.Arg170His"
}
],
"clinvar_disease": " autosomal recessive 34,Intellectual disability,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Intellectual disability, autosomal recessive 34|Intellectual disability|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}