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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: 12-105164239-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=105164239&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 105164239,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000332180.10",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WASHC4",
"gene_hgnc_id": 29174,
"hgvs_c": "c.3286G>A",
"hgvs_p": "p.Ala1096Thr",
"transcript": "NM_015275.3",
"protein_id": "NP_056090.1",
"transcript_support_level": null,
"aa_start": 1096,
"aa_end": null,
"aa_length": 1173,
"cds_start": 3286,
"cds_end": null,
"cds_length": 3522,
"cdna_start": 3356,
"cdna_end": null,
"cdna_length": 5791,
"mane_select": "ENST00000332180.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WASHC4",
"gene_hgnc_id": 29174,
"hgvs_c": "c.3286G>A",
"hgvs_p": "p.Ala1096Thr",
"transcript": "ENST00000332180.10",
"protein_id": "ENSP00000328062.6",
"transcript_support_level": 1,
"aa_start": 1096,
"aa_end": null,
"aa_length": 1173,
"cds_start": 3286,
"cds_end": null,
"cds_length": 3522,
"cdna_start": 3356,
"cdna_end": null,
"cdna_length": 5791,
"mane_select": "NM_015275.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WASHC4",
"gene_hgnc_id": 29174,
"hgvs_c": "c.3289G>A",
"hgvs_p": "p.Ala1097Thr",
"transcript": "ENST00000620430.5",
"protein_id": "ENSP00000484713.1",
"transcript_support_level": 1,
"aa_start": 1097,
"aa_end": null,
"aa_length": 1174,
"cds_start": 3289,
"cds_end": null,
"cds_length": 3525,
"cdna_start": 3318,
"cdna_end": null,
"cdna_length": 3623,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WASHC4",
"gene_hgnc_id": 29174,
"hgvs_c": "c.3289G>A",
"hgvs_p": "p.Ala1097Thr",
"transcript": "NM_001293640.2",
"protein_id": "NP_001280569.1",
"transcript_support_level": null,
"aa_start": 1097,
"aa_end": null,
"aa_length": 1174,
"cds_start": 3289,
"cds_end": null,
"cds_length": 3525,
"cdna_start": 3359,
"cdna_end": null,
"cdna_length": 5794,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WASHC4",
"gene_hgnc_id": 29174,
"hgvs_c": "c.3151G>A",
"hgvs_p": "p.Ala1051Thr",
"transcript": "XM_011538073.4",
"protein_id": "XP_011536375.1",
"transcript_support_level": null,
"aa_start": 1051,
"aa_end": null,
"aa_length": 1128,
"cds_start": 3151,
"cds_end": null,
"cds_length": 3387,
"cdna_start": 3221,
"cdna_end": null,
"cdna_length": 5656,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WASHC4",
"gene_hgnc_id": 29174,
"hgvs_c": "c.2722G>A",
"hgvs_p": "p.Ala908Thr",
"transcript": "XM_011538074.3",
"protein_id": "XP_011536376.1",
"transcript_support_level": null,
"aa_start": 908,
"aa_end": null,
"aa_length": 985,
"cds_start": 2722,
"cds_end": null,
"cds_length": 2958,
"cdna_start": 2829,
"cdna_end": null,
"cdna_length": 5264,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WASHC4",
"gene_hgnc_id": 29174,
"hgvs_c": "n.226G>A",
"hgvs_p": null,
"transcript": "ENST00000547171.1",
"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": 351,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "WASHC4",
"gene_hgnc_id": 29174,
"hgvs_c": "n.184G>A",
"hgvs_p": null,
"transcript": "ENST00000550036.1",
"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": 578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WASHC4",
"gene_hgnc_id": 29174,
"hgvs_c": "n.*2728G>A",
"hgvs_p": null,
"transcript": "ENST00000550053.5",
"protein_id": "ENSP00000448966.1",
"transcript_support_level": 5,
"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": 5819,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WASHC4",
"gene_hgnc_id": 29174,
"hgvs_c": "n.*2728G>A",
"hgvs_p": null,
"transcript": "ENST00000550053.5",
"protein_id": "ENSP00000448966.1",
"transcript_support_level": 5,
"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": 5819,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "WASHC4",
"gene_hgnc_id": 29174,
"dbsnp": "rs113168943",
"frequency_reference_population": 0.000053901476,
"hom_count_reference_population": 0,
"allele_count_reference_population": 87,
"gnomad_exomes_af": 0.0000403624,
"gnomad_genomes_af": 0.00018385,
"gnomad_exomes_ac": 59,
"gnomad_genomes_ac": 28,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.006246685981750488,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.172,
"revel_prediction": "Benign",
"alphamissense_score": 0.0614,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.57,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.021,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000332180.10",
"gene_symbol": "WASHC4",
"hgnc_id": 29174,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.3286G>A",
"hgvs_p": "p.Ala1096Thr"
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:1",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}